Chargement des library

importation de la base de données

enlever les espaces sur les entêtes, filtrer les années à juste celle 2023, nettoyer dans la colonne region le fait que:(Centre= CENTRE, Sud= sud)

llcholeraclean <- llcholera110124 %>% 
  mutate(
    annee = substring(epiweek_date_notification_2, 5, 8)
  ) %>% 
  filter(annee == "2023") %>% 
  mutate(region_34 = ifelse(region_34=="CENTRE", "Centre", ifelse(region_34=="sud", "Sud", region_34)))

creer un tableau avec les variables qui m’interessent

llcholeraclean <- llcholeraclean %>% 
  select(c("n_id_1", "epiweek_date_notification_2", "health_district_of_origin", "age_year_6", "sex_7", "hospitalisation_oui_non", "region_34", "health_district_notifying_13", "state_of_dehydratation_1_mild_2_moderate_3_severe_16",  "site_of_case_management", "result_of_culture", "outcome_2_healed_3_dead_32", "hospitalisation_oui_non"))

ajouter les colonnes Cas et Décès et cas confirmés par cultures (avec chacun des references spécifiques)

  llcholeraclean <- llcholeraclean %>%
  mutate(deces = ifelse(outcome_2_healed_3_dead_32 != 3, "vivant", "mort")) %>% 
  mutate(deces = ifelse(is.na(outcome_2_healed_3_dead_32), "vivant", deces))

histogramme en facte-grid par région du niveau de sérvérité(la colonne state_of_dehydratation) en focntion des semaines épidémiologique(epiweek_date-notification_2) pour comparaison

llcholeraclean$state_of_dehydratation_1_mild_2_moderate_3_severe_16[ is.na(llcholeraclean$state_of_dehydratation_1_mild_2_moderate_3_severe_16)] <- 2
ggplot(llcholeraclean, aes(y = epiweek_date_notification_2, fill = factor(state_of_dehydratation_1_mild_2_moderate_3_severe_16))) +
  geom_bar(stat = "count", position = "stack") +
  facet_grid(rows = vars(region_34)) +
  scale_fill_manual(values = c("1" = "green", "2" = "yellow", "3" = "red"),
                    name = "Niveau de sévérité",
                    labels = c("1" = "Légère", "2" = "Modérée", "3" = "Sévère")) +
  labs(title = "Variation de la sévérité par région en fonction des semaines épidémiologiques",
       x = "Niveau",
       y = "Semaine épidémiologique") +
  theme_minimal() +
  coord_flip() +
  theme(axis.text.x = element_text(angle = 90, hjust = 1))

Nous observons sur le graphique en facet-grid prensentant le niveau de sévérité que l’épidémie a débuté de manière continue dès la première semaine jusqu’à la 52e semaine de l’année, tant au Centre qu’au littoral. Cependant, une caractéristique distincte émerge : la courbe révèle un taux de sévérité significatif au stade élevé entre la semaine 15 et la semaine 24 dans ces deux régions. En examinant les autres régions, nous constatons que dans le Sud, les cas se font ressentir entre la semaine 16 et la semaine 27. Parallèlement, le Sud-Ouest affiche une hausse des cas notable de la semaine 32 à la semaine 45. Il est intéressant de noter que cette augmentation peut suggérer une possible importation de cas de la région du littoral vers le Sud-Ouest, probablement due à leur proximité géographique. Cette analyse temporelle met en lumière des variations régionales dans la dynamique de l’épidémie, soulignant la nécessité d’une approche différenciée pour les interventions et la surveillance épidémiologique.

sévétité pour la region du Centre

ggplot(subset(llcholeraclean, region_34 == "Centre"),
       aes(y = epiweek_date_notification_2, fill = factor(state_of_dehydratation_1_mild_2_moderate_3_severe_16))) +
  geom_bar(stat = "count", position = "stack") +
  scale_fill_manual(values = c("1" = "green", "2" = "yellow", "3" = "red"),
                    name = "Niveau de sévérité",
                    labels = c("1" = "Légère", "2" = "Modérée", "3" = "Sévère")) +
  labs(title = "Variation de la sévérité pour la région du Centre en fonction des semaines épidémiologiques",
       x = "Niveau",
       y = "Semaine épidémiologique") +
  theme_minimal() +
  coord_flip() +
  theme(axis.text.x = element_text(angle = 90, hjust = 1),
        legend.position = "bottom",  # Positionner la légende en bas
        legend.direction = "horizontal") +
  facet_wrap(~region_34, scales = "free_y", ncol = 1)

Pendant les semaines 13 à 37, on observe une nette flambée des cas dans la région du Centre, avec un pic de sévérité entre la semaine 16 et 26. Cette augmentation significative conduit à un nombre croissant de patients se présentant en clinique, principalement à un stade modéré de l’épidémie. La dynamique du graphe met en lumière l’urgence de mesures préventives et de gestion pour faire face à cette hausse soudaine de la gravité des cas.

sévérité pour le Littoral

ggplot(subset(llcholeraclean, region_34 == "Littoral"),
       aes(y = epiweek_date_notification_2, fill = factor(state_of_dehydratation_1_mild_2_moderate_3_severe_16))) +
  geom_bar(stat = "count", position = "stack") +
  scale_fill_manual(values = c("1" = "green", "2" = "yellow", "3" = "red"),
                    name = "Niveau de sévérité",
                    labels = c("1" = "Légère", "2" = "Modérée", "3" = "Sévère")) +
  labs(title = "Variation de la sévérité pour la région du Littoral en fonction des semaines épidémiologiques",
       x = "Niveau",
       y = "Semaine épidémiologique") +
  theme_minimal() +
  coord_flip() +
  theme(axis.text.x = element_text(angle = 90, hjust = 1),
        legend.position = "bottom",  # Positionner la légende en bas
        legend.direction = "horizontal") +
  facet_wrap(~region_34, scales = "free_y", ncol = 1)

Au cours des semaines 1 à 27 dans la région du littoral, une évolution régulière des cas a été constatée. Cependant, à partir de la semaine 28 jusqu’à la 44, une flambée considérable a émergé, marquée par une augmentation significative des cas. Cette tendance abrupte souligne l’importance d’une réponse rapide et ciblée pour atténuer l’impact croissant de la situation dans la région.

Sévérité pour l’Ouest

ggplot(subset(llcholeraclean, region_34 == "Ouest"),
       aes(y = epiweek_date_notification_2, fill = factor(state_of_dehydratation_1_mild_2_moderate_3_severe_16))) +
  geom_bar(stat = "count", position = "stack") +
  scale_fill_manual(values = c("1" = "green", "2" = "yellow", "3" = "red"),
                    name = "Niveau de sévérité",
                    labels = c("1" = "Légère", "2" = "Modérée", "3" = "Sévère")) +
  labs(title = "Variation de la sévérité pour la région du Ouest en fonction des semaines épidémiologiques",
       x = "Niveau",
       y = "Semaine épidémiologique") +
  theme_minimal() +
  coord_flip() +
  theme(axis.text.x = element_text(angle = 90, hjust = 1),
        legend.position = "bottom",  # Positionner la légende en bas
        legend.direction = "horizontal") +
  facet_wrap(~region_34, scales = "free_y", ncol = 1)

Dans la région de l’Ouest, l’évolution des cas de choléra entre la semaine 4 et la semaine 33 est remarquable. Notamment, des pics de taux sévères sont observés aux semaines 7, 13, 14, et 30, mettant en évidence des moments critiques au cours de cette période. Le reste de la courbe indique principalement des cas modérés, soulignant la nécessité d’une vigilance particulière pour contrôler la gravité de la maladie dans la région.

Sévérité pour le Sud-Ouest

ggplot(subset(llcholeraclean, region_34 == "Sud-Ouest"),
       aes(y = epiweek_date_notification_2, fill = factor(state_of_dehydratation_1_mild_2_moderate_3_severe_16))) +
  geom_bar(stat = "count", position = "stack") +
  scale_fill_manual(values = c("1" = "green", "2" = "yellow", "3" = "red"),
                    name = "Niveau de sévérité",
                    labels = c("1" = "Légère", "2" = "Modérée", "3" = "Sévère")) +
  labs(title = "Variation de la sévérité pour la région du Sud-Ouest en fonction des semaines épidémiologiques",
       x = "Niveau",
       y = "Semaine épidémiologique") +
  theme_minimal() +
  coord_flip() +
  theme(axis.text.x = element_text(angle = 90, hjust = 1),
        legend.position = "bottom",  # Positionner la légende en bas
        legend.direction = "horizontal") +
  facet_wrap(~region_34, scales = "free_y", ncol = 1)

Sévérité pour le Sud

ggplot(subset(llcholeraclean, region_34 == "Sud"),
       aes(y = epiweek_date_notification_2, fill = factor(state_of_dehydratation_1_mild_2_moderate_3_severe_16))) +
  geom_bar(stat = "count", position = "stack") +
  scale_fill_manual(values = c("1" = "green", "2" = "yellow", "3" = "red"),
                    name = "Niveau de sévérité",
                    labels = c("1" = "Légère", "2" = "Modérée", "3" = "Sévère")) +
  labs(title = "Variation de la sévérité pour la région du Sud en fonction des semaines épidémiologiques",
       x = "Niveau",
       y = "Semaine épidémiologique") +
  theme_minimal() +
  coord_flip() +
  theme(axis.text.x = element_text(angle = 90, hjust = 1),
        legend.position = "bottom",  # Positionner la légende en bas
        legend.direction = "horizontal") +
  facet_wrap(~region_34, scales = "free_y", ncol = 1)

Repartition des Cas et Deces par région en 2023

I-Creons en primaire une colonne Cas dans notre jeu de donnée

llcholeraclean <- llcholeraclean %>% 
  mutate(cas = ifelse(!is.na(n_id_1), 1, 0))

Convertir les cas et deces en numeric pour pouvoir afficher

llcholeraclean$cas <- as.numeric(as.character(llcholeraclean$cas))
llcholeraclean$deces <- as.numeric(as.character(llcholeraclean$deces))
## Warning: NAs introduced by coercion

copnvertir pour enlever les valeurs manquante par 0

llcholeraclean$cas[is.na(llcholeraclean$cas)] <- 0
llcholeraclean$deces[is.na(llcholeraclean$deces)] <- 0

##Courbe representative des cas (regions: centre, littoral, sud, sud-Ouet et Ouest)

llcholeraclean %>%
 filter(!(region_34 %in% c("Est", "Nord-Ouest"))) %>%
 ggplot() +
 aes(x = epiweek_date_notification_2, fill = region_34) +
 geom_bar() +
 scale_fill_manual(values = c(Centre = "red",
Est = "#BD9A00", Littoral = "#31B425", `Nord-Ouest` = "#00C19F", Ouest = "blue", Sud = "#B280FC" , 
`Sud-Ouest` = "#FF61C3" )) +
 labs(x = "Semaine épidémiologique", y = "Nombre de décès ", title = " Évolution des décès au cours de l'année 2023", 
 fill = "Régions") +
 theme_minimal() +
 theme(plot.title = element_text(size = 20L, face = "bold", 
 hjust = 0.5)) +
   theme(axis.text.x = element_text(angle = 90, hjust = 1))+
 facet_grid(vars(deces))

L’évolution des cas et décès dans les 10 régions du Cameroun montre des disparités significatives. La région du Centre se démarque avec le plus grand nombre de décès, totalisant 159 pour l’année 2023, et un taux de létalité de 3,4%. Cela souligne la nécessité de mesures renforcées dans cette région pour contenir la situation. Le littoral suit avec 31 décès et un taux de létalité de 2,1%. Cependant, le Sud, bien que présentant un nombre moindre de décès (9), affiche un taux de létalité élevé de 9,5%, soulignant une situation plus critique compte tenu de sa population de 953 923 habitants. Cette variation souligne l’importance d’analyses approfondies pour comprendre les différences dans la mortalité et adapter les stratégies en conséquence.

SITUATION DES DECES DES REGIONS CENTRE ET LITTORAL EN FOCTION DE L’ADMISSION EN HOSPITALISATION

Du fait que, d’après le graphe ci dessus, les deux regions ayants le taux de letalité le plus elevé sont le Centre et Littoral, ressortont pour chacun leur histogramme en fonction de l’admission en hospitalisation ou pas

1- verifions s’il y’a des valeurs autres que “oui” et “non” dans la colonne “hospitalisation_oui_non”

unique(llcholeraclean$hospitalisation_oui_non)
##  [1] "Oui"           "OUI"           NA              "NON"          
##  [5] "Non"           "non"           "oui"           "0"            
##  [9] "ARIVEE DECEDE" "YES"           "NO"            "oUI"          
## [13] "yes"

2- Remplacons les intrus par les correspondants initiaux( soit ‘oui’ ou “non”)

llcholeraclean <- llcholeraclean %>%
  mutate(hospitalisation_oui_non = case_when(
    hospitalisation_oui_non %in% c("OUI", "oUI", "yes", "YES", "Oui") ~ "oui",
    TRUE ~ hospitalisation_oui_non
  ))
llcholeraclean <- llcholeraclean %>%
  mutate(hospitalisation_oui_non = case_when(
    hospitalisation_oui_non %in% c("NO", "Non", "NON", "0") ~ "non",
    TRUE ~ hospitalisation_oui_non
  ))

3-Convertir les valeurs manquantes par “0”

llcholeraclean$hospitalisation_oui_non[is.na(llcholeraclean$hospitalisation_oui_non)] <- 0

4-Puis remplacer “0” par “non”

llcholeraclean <- llcholeraclean %>%
  mutate(hospitalisation_oui_non = ifelse(
    hospitalisation_oui_non == "0", "non", hospitalisation_oui_non))

5- Remplacer “ARIVEEDECEDE” par “non” dans la colonne “hospitalisation_oui_non”

llcholeraclean <- llcholeraclean %>%
  mutate(hospitalisation_oui_non = ifelse(
    hospitalisation_oui_non == "ARIVEE DECEDE", "non", hospitalisation_oui_non))

6- Tracé de ladite courbe

llcholeraclean %>%
 filter(region_34 %in% c("Centre", "Littoral")) %>%
 ggplot() +
  aes(
    x = epiweek_date_notification_2,
    fill = hospitalisation_oui_non
  ) +
  geom_bar() +
  scale_fill_hue(direction = 1) + 
  labs(
    x = "Semaines épidémiologiques",
    y = "Nombre de décès",
    title = " Cumul d'évolution des décès dans les Régions: centre et Littoral",
    subtitle = "Répartition des hospitalisés ou pas "
  ) +
  theme_minimal() +
  theme(
    plot.title = element_text(size = 20L,
    face = "bold",
    hjust = 0.5),
    plot.subtitle = element_text(size = 12L,
    face = "bold"),
    axis.title.y = element_text(size = 12L,
    face = "bold"),
    axis.title.x = element_text(size = 12L, 
    ))+
 theme(axis.text.x = element_text(angle = 90, hjust = 1))+
  facet_grid(vars(deces)) 

importer la base pour les vulnerabilités wash et nettoyer les noms pour enlever les espaces (enquête evidences base cholera dans les regions Centre et Littoeral

ebasecholera <- import(here("ebasecholera.xlsx")) %>% 
  clean_names()
## New names:
## • `Préciser` -> `Préciser...7`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...8`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...9`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...10`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...11`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...12`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...13`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...14`
## • `1.2. Par quel canal?` -> `1.2. Par quel canal?...42`
## • `Preciser` -> `Preciser...88`
## • `Préciser` -> `Préciser...102`
## • `Préciser` -> `Préciser...119`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...141`
## • `5. AIRE DE SANTÉ` -> `5. AIRE DE SANTÉ...142`
## • `1.2. Par quel canal?` -> `1.2. Par quel canal?...143`
## • `_id` -> `_id...144`
## • `_uuid` -> `_uuid...145`
## • `_submission_time` -> `_submission_time...146`
## • `_validation_status` -> `_validation_status...147`
## • `_notes` -> `_notes...148`
## • `_status` -> `_status...149`
## • `_submitted_by` -> `_submitted_by...150`
## • `__version__` -> `__version__...151`
## • `_tags` -> `_tags...152`
## • `_index` -> `_index...153`
## • `Environnement du ménage/Présence d’eaux usées` -> `Environnement du
##   ménage/Présence d’eaux usées...168`
## • `Environnement du ménage/Présence d’eaux usées` -> `Environnement du
##   ménage/Présence d’eaux usées...169`
## • `Preciser` -> `Preciser...179`
## • `Preciser` -> `Preciser...188`
## • `Preciser` -> `Preciser...190`
## • `Preciser` -> `Preciser...192`
## • `_id` -> `_id...197`
## • `_uuid` -> `_uuid...198`
## • `_submission_time` -> `_submission_time...199`
## • `_validation_status` -> `_validation_status...200`
## • `_notes` -> `_notes...201`
## • `_status` -> `_status...202`
## • `_submitted_by` -> `_submitted_by...203`
## • `__version__` -> `__version__...204`
## • `_tags` -> `_tags...205`
## • `_index` -> `_index...206`
summary(ebasecholera)
##   x1_numero            x2_date                       x3_region        
##  Length:1459        Min.   :2023-07-18 00:00:00.0   Length:1459       
##  Class :character   1st Qu.:2023-07-20 00:00:00.0   Class :character  
##  Mode  :character   Median :2023-07-21 00:00:00.0   Mode  :character  
##                     Mean   :2023-07-20 14:45:25.0                     
##                     3rd Qu.:2023-07-21 00:00:00.0                     
##                     Max.   :2023-07-24 00:00:00.0                     
##                     NA's   :706                                       
##  x4_district_de_sante aire_de_sante_djoungolo aire_de_sante_efoulan
##  Length:1459          Length:1459             Length:1459          
##  Class :character     Class :character        Class :character     
##  Mode  :character     Mode  :character        Mode  :character     
##                                                                    
##                                                                    
##                                                                    
##                                                                    
##   preciser_7        x5_aire_de_sante_8 x5_aire_de_sante_9 x5_aire_de_sante_10
##  Length:1459        Length:1459        Length:1459        Length:1459        
##  Class :character   Class :character   Class :character   Class :character   
##  Mode  :character   Mode  :character   Mode  :character   Mode  :character   
##                                                                              
##                                                                              
##                                                                              
##                                                                              
##  x5_aire_de_sante_11 x5_aire_de_sante_12 x5_aire_de_sante_13
##  Length:1459         Length:1459         Length:1459        
##  Class :character    Class :character    Class :character   
##  Mode  :character    Mode  :character    Mode  :character   
##                                                             
##                                                             
##                                                             
##                                                             
##  x5_aire_de_sante_14 i_as_d_etoua_meki  ii_as_de_mballa_2  iii_as_d_emana    
##  Length:1459         Length:1459        Length:1459        Length:1459       
##  Class :character    Class :character   Class :character   Class :character  
##  Mode  :character    Mode  :character   Mode  :character   Mode  :character  
##                                                                              
##                                                                              
##                                                                              
##                                                                              
##  iv_as_de_tsinga_village v_as_de_nlongkak   vi_as_de_mballa_5 
##  Length:1459             Length:1459        Length:1459       
##  Class :character        Class :character   Class :character  
##  Mode  :character        Mode  :character   Mode  :character  
##                                                               
##                                                               
##                                                               
##                                                               
##  vii_as_de_nkonldom iix_as_d_elig_essono   as_1           as_ahala        
##  Length:1459        Length:1459          Mode:logical   Length:1459       
##  Class :character   Class :character     NA's:1459      Class :character  
##  Mode  :character   Mode  :character                    Mode  :character  
##                                                                           
##                                                                           
##                                                                           
##                                                                           
##   as_ahala_2        as_nsimeyong_2     as_nsiemeyong_3    as_obili      
##  Length:1459        Length:1459        Length:1459        Mode:logical  
##  Class :character   Class :character   Class :character   NA's:1459     
##  Mode  :character   Mode  :character   Mode  :character                 
##                                                                         
##                                                                         
##                                                                         
##                                                                         
##    x6_fosa          x7_disponibilite_des_points_deau x8_coordonnees_gps
##  Length:1459        Length:1459                      Length:1459       
##  Class :character   Class :character                 Class :character  
##  Mode  :character   Mode  :character                 Mode  :character  
##                                                                        
##                                                                        
##                                                                        
##                                                                        
##  x8_coordonnees_gps_latitude x8_coordonnees_gps_longitude
##  Min.   :3.768               Min.   :11.43               
##  1st Qu.:3.848               1st Qu.:11.50               
##  Median :3.869               Median :11.52               
##  Mean   :3.872               Mean   :11.52               
##  3rd Qu.:3.887               3rd Qu.:11.54               
##  Max.   :4.057               Max.   :11.61               
##  NA's   :768                 NA's   :768                 
##  x8_coordonnees_gps_altitude x8_coordonnees_gps_precision     x1_age      
##  Min.   :-213.7              Min.   :   3.0               Min.   :  18.0  
##  1st Qu.:   0.0              1st Qu.:  20.0               1st Qu.:  29.0  
##  Median : 728.8              Median :  77.6               Median :  33.0  
##  Mean   : 520.8              Mean   : 662.9               Mean   :  49.6  
##  3rd Qu.: 755.9              3rd Qu.:1600.0               3rd Qu.:  40.0  
##  Max.   :1201.0              Max.   :7067.2               Max.   :5123.0  
##  NA's   :768                 NA's   :768                  NA's   :711     
##    x2_sexe          x3_anciennete_de_service  x4_profil        
##  Length:1459        Min.   :       -8        Length:1459       
##  Class :character   1st Qu.:        2        Class :character  
##  Mode  :character   Median :        4        Mode  :character  
##                     Mean   :   549463                          
##                     3rd Qu.:        9                          
##                     Max.   :400002023                          
##                     NA's   :731                                
##  x5_preciser        x1_avez_vous_entendu_parler_du_cholera
##  Length:1459        Length:1459                           
##  Class :character   Class :character                      
##  Mode  :character   Mode  :character                      
##                                                           
##                                                           
##                                                           
##                                                           
##  x1_2_par_quel_canal_42 x1_2_par_quel_canal_presse x1_2_par_quel_canal_radio
##  Length:1459            Min.   :0.0                Min.   :0.000            
##  Class :character       1st Qu.:0.0                1st Qu.:0.000            
##  Mode  :character       Median :0.0                Median :1.000            
##                         Mean   :0.4                Mean   :0.519            
##                         3rd Qu.:1.0                3rd Qu.:1.000            
##                         Max.   :1.0                Max.   :1.000            
##                         NA's   :879                NA's   :879              
##  x1_2_par_quel_canal_television x1_2_par_quel_canal_crieur_asc
##  Min.   :0.0000                 Min.   :0.0000                
##  1st Qu.:0.0000                 1st Qu.:0.0000                
##  Median :1.0000                 Median :0.0000                
##  Mean   :0.6569                 Mean   :0.1017                
##  3rd Qu.:1.0000                 3rd Qu.:0.0000                
##  Max.   :1.0000                 Max.   :1.0000                
##  NA's   :879                    NA's   :879                   
##  x1_2_par_quel_canal_personnel_de_sante
##  Min.   :0.0000                        
##  1st Qu.:0.0000                        
##  Median :1.0000                        
##  Mean   :0.6948                        
##  3rd Qu.:1.0000                        
##  Max.   :1.0000                        
##  NA's   :879                           
##  x1_2_par_quel_canal_pendant_une_formation
##  Min.   :0.0000                           
##  1st Qu.:0.0000                           
##  Median :0.0000                           
##  Mean   :0.4897                           
##  3rd Qu.:1.0000                           
##  Max.   :1.0000                           
##  NA's   :879                              
##  x2_connaissez_vous_la_definition_des_cas_du_cholera
##  Length:1459                                        
##  Class :character                                   
##  Mode  :character                                   
##                                                     
##                                                     
##                                                     
##                                                     
##  x4_quelle_est_la_definition_des_cas_suspect_de_cholera
##  Length:1459                                           
##  Class :character                                      
##  Mode  :character                                      
##                                                        
##                                                        
##                                                        
##                                                        
##  definition_des_cas_corrects_ou_pas x5_comment_se_transmet_il
##  Length:1459                        Length:1459              
##  Class :character                   Class :character         
##  Mode  :character                   Mode  :character         
##                                                              
##                                                              
##                                                              
##                                                              
##  x5_comment_se_transmet_il_rapports_sexuels
##  Min.   :0.0000                            
##  1st Qu.:0.0000                            
##  Median :0.0000                            
##  Mean   :0.0066                            
##  3rd Qu.:0.0000                            
##  Max.   :1.0000                            
##  NA's   :705                               
##  x5_comment_se_transmet_il_consommation_dune_eau_non_potable
##  Min.   :0.000                                              
##  1st Qu.:1.000                                              
##  Median :1.000                                              
##  Mean   :0.882                                              
##  3rd Qu.:1.000                                              
##  Max.   :1.000                                              
##  NA's   :705                                                
##  x5_comment_se_transmet_il_manipulation_des_objets_souilles
##  Min.   :0.0000                                            
##  1st Qu.:0.0000                                            
##  Median :0.0000                                            
##  Mean   :0.3912                                            
##  3rd Qu.:1.0000                                            
##  Max.   :1.0000                                            
##  NA's   :705                                               
##  x5_comment_se_transmet_il_consommation_des_aliments_soulles
##  Min.   :0.0000                                             
##  1st Qu.:1.0000                                             
##  Median :1.0000                                             
##  Mean   :0.9125                                             
##  3rd Qu.:1.0000                                             
##  Max.   :1.0000                                             
##  NA's   :705                                                
##  x5_comment_se_transmet_il_piqure_dinsecte
##  Min.   :0.0000                           
##  1st Qu.:0.0000                           
##  Median :0.0000                           
##  Mean   :0.0119                           
##  3rd Qu.:0.0000                           
##  Max.   :1.0000                           
##  NA's   :705                              
##  x5_comment_se_transmet_il_repas_contamines x5_comment_se_transmet_il_nsp
##  Min.   :0.0000                             Min.   :0.0000               
##  1st Qu.:0.0000                             1st Qu.:0.0000               
##  Median :1.0000                             Median :0.0000               
##  Mean   :0.6313                             Mean   :0.0119               
##  3rd Qu.:1.0000                             3rd Qu.:0.0000               
##  Max.   :1.0000                             Max.   :1.0000               
##  NA's   :705                                NA's   :705                  
##  x6_comment_reconnaissez_vous_les_cas_suspects_de_cholera
##  Length:1459                                             
##  Class :character                                        
##  Mode  :character                                        
##                                                          
##                                                          
##                                                          
##                                                          
##  x6_comment_reconnaissez_vous_les_cas_suspects_de_cholera_fatigue
##  Min.   :0.0000                                                  
##  1st Qu.:0.0000                                                  
##  Median :1.0000                                                  
##  Mean   :0.6662                                                  
##  3rd Qu.:1.0000                                                  
##  Max.   :1.0000                                                  
##  NA's   :704                                                     
##  x6_comment_reconnaissez_vous_les_cas_suspects_de_cholera_jaunisse
##  Min.   :0.0000                                                   
##  1st Qu.:0.0000                                                   
##  Median :0.0000                                                   
##  Mean   :0.0106                                                   
##  3rd Qu.:0.0000                                                   
##  Max.   :1.0000                                                   
##  NA's   :704                                                      
##  x6_comment_reconnaissez_vous_les_cas_suspects_de_cholera_diarrhee
##  Min.   :0.0000                                                   
##  1st Qu.:1.0000                                                   
##  Median :1.0000                                                   
##  Mean   :0.9788                                                   
##  3rd Qu.:1.0000                                                   
##  Max.   :1.0000                                                   
##  NA's   :704                                                      
##  x6_comment_reconnaissez_vous_les_cas_suspects_de_cholera_soif_intense
##  Min.   :0.0000                                                       
##  1st Qu.:0.0000                                                       
##  Median :0.0000                                                       
##  Mean   :0.4318                                                       
##  3rd Qu.:1.0000                                                       
##  Max.   :1.0000                                                       
##  NA's   :704                                                          
##  x6_comment_reconnaissez_vous_les_cas_suspects_de_cholera_deshydratation
##  Min.   :0.0000                                                         
##  1st Qu.:1.0000                                                         
##  Median :1.0000                                                         
##  Mean   :0.8079                                                         
##  3rd Qu.:1.0000                                                         
##  Max.   :1.0000                                                         
##  NA's   :704                                                            
##  x6_comment_reconnaissez_vous_les_cas_suspects_de_cholera_vomissements
##  Min.   :0.0000                                                       
##  1st Qu.:1.0000                                                       
##  Median :1.0000                                                       
##  Mean   :0.9338                                                       
##  3rd Qu.:1.0000                                                       
##  Max.   :1.0000                                                       
##  NA's   :704                                                          
##  x6_comment_reconnaissez_vous_les_cas_suspects_de_cholera_nsp
##  Min.   :0.0000                                              
##  1st Qu.:0.0000                                              
##  Median :0.0000                                              
##  Mean   :0.0106                                              
##  3rd Qu.:0.0000                                              
##  Max.   :1.0000                                              
##  NA's   :704                                                 
##  x7_la_definition_des_cas_de_cholera_est_elle_differente_en_cas_d_epidemie_et_en_dehors_de_l_epidemie
##  Length:1459                                                                                         
##  Class :character                                                                                    
##  Mode  :character                                                                                    
##                                                                                                      
##                                                                                                      
##                                                                                                      
##                                                                                                      
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera
##  Length:1459                                                            
##  Class :character                                                       
##  Mode  :character                                                       
##                                                                         
##                                                                         
##                                                                         
##                                                                         
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera_laver_le_visage
##  Min.   :0.0000                                                                         
##  1st Qu.:0.0000                                                                         
##  Median :0.0000                                                                         
##  Mean   :0.0226                                                                         
##  3rd Qu.:0.0000                                                                         
##  Max.   :1.0000                                                                         
##  NA's   :706                                                                            
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera_laver_les_mains
##  Min.   :0.0000                                                                         
##  1st Qu.:1.0000                                                                         
##  Median :1.0000                                                                         
##  Mean   :0.9841                                                                         
##  3rd Qu.:1.0000                                                                         
##  Max.   :1.0000                                                                         
##  NA's   :706                                                                            
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera_laver_les_habits
##  Min.   :0.0000                                                                          
##  1st Qu.:0.0000                                                                          
##  Median :0.0000                                                                          
##  Mean   :0.1912                                                                          
##  3rd Qu.:0.0000                                                                          
##  Max.   :1.0000                                                                          
##  NA's   :706                                                                             
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera_boire_la_doxycycline
##  Min.   :0.0000                                                                              
##  1st Qu.:0.0000                                                                              
##  Median :0.0000                                                                              
##  Mean   :0.3121                                                                              
##  3rd Qu.:1.0000                                                                              
##  Max.   :1.0000                                                                              
##  NA's   :706                                                                                 
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera_desinfecter_les_puits
##  Min.   :0.0000                                                                               
##  1st Qu.:0.0000                                                                               
##  Median :1.0000                                                                               
##  Mean   :0.7224                                                                               
##  3rd Qu.:1.0000                                                                               
##  Max.   :1.0000                                                                               
##  NA's   :706                                                                                  
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera_lavage_des_aliments
##  Min.   :0.0000                                                                             
##  1st Qu.:1.0000                                                                             
##  Median :1.0000                                                                             
##  Mean   :0.9057                                                                             
##  3rd Qu.:1.0000                                                                             
##  Max.   :1.0000                                                                             
##  NA's   :706                                                                                
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera_lavage_du_sol_a_leau_de_javel
##  Min.   :0.0000                                                                                       
##  1st Qu.:0.0000                                                                                       
##  Median :1.0000                                                                                       
##  Mean   :0.6029                                                                                       
##  3rd Qu.:1.0000                                                                                       
##  Max.   :1.0000                                                                                       
##  NA's   :706                                                                                          
##  x8_quelles_mesures_doit_on_prendre_pour_eviter_de_contracter_le_cholera_utilisation_des_toilettes_amenagees
##  Min.   :0.0000                                                                                             
##  1st Qu.:0.0000                                                                                             
##  Median :1.0000                                                                                             
##  Mean   :0.6524                                                                                             
##  3rd Qu.:1.0000                                                                                             
##  Max.   :1.0000                                                                                             
##  NA's   :875                                                                                                
##  x9_savez_vous_classer_les_cas_de_cholera_en_fonction_du_niveau_de_deshydratation
##  Length:1459                                                                     
##  Class :character                                                                
##  Mode  :character                                                                
##                                                                                  
##                                                                                  
##                                                                                  
##                                                                                  
##  x10_quel_sont_les_differents_stades_de_deshydratation_que_vous_connaissez
##  Length:1459                                                              
##  Class :character                                                         
##  Mode  :character                                                         
##                                                                           
##                                                                           
##                                                                           
##                                                                           
##  x10_quel_sont_les_differents_stades_de_deshydratation_que_vous_connaissez_legere
##  Min.   :0.0000                                                                  
##  1st Qu.:1.0000                                                                  
##  Median :1.0000                                                                  
##  Mean   :0.8428                                                                  
##  3rd Qu.:1.0000                                                                  
##  Max.   :1.0000                                                                  
##  NA's   :842                                                                     
##  x10_quel_sont_les_differents_stades_de_deshydratation_que_vous_connaissez_modere
##  Min.   :0.0000                                                                  
##  1st Qu.:1.0000                                                                  
##  Median :1.0000                                                                  
##  Mean   :0.8525                                                                  
##  3rd Qu.:1.0000                                                                  
##  Max.   :1.0000                                                                  
##  NA's   :842                                                                     
##  x10_quel_sont_les_differents_stades_de_deshydratation_que_vous_connaissez_severe
##  Min.   :0.0000                                                                  
##  1st Qu.:1.0000                                                                  
##  Median :1.0000                                                                  
##  Mean   :0.8509                                                                  
##  3rd Qu.:1.0000                                                                  
##  Max.   :1.0000                                                                  
##  NA's   :842                                                                     
##  x10_quel_sont_les_differents_stades_de_deshydratation_que_vous_connaissez_grave
##  Min.   :0.0000                                                                 
##  1st Qu.:0.0000                                                                 
##  Median :0.0000                                                                 
##  Mean   :0.1767                                                                 
##  3rd Qu.:0.0000                                                                 
##  Max.   :1.0000                                                                 
##  NA's   :842                                                                    
##  x10_quel_sont_les_differents_stades_de_deshydratation_que_vous_connaissez_chronique
##  Min.   :0.0000                                                                     
##  1st Qu.:0.0000                                                                     
##  Median :0.0000                                                                     
##  Mean   :0.0859                                                                     
##  3rd Qu.:0.0000                                                                     
##  Max.   :1.0000                                                                     
##  NA's   :842                                                                        
##  x11_quel_est_le_traitement_du_cholera
##  Length:1459                          
##  Class :character                     
##  Mode  :character                     
##                                       
##                                       
##                                       
##                                       
##  x12_quel_prelevement_faut_il_faire_en_cas_de_suspicion_de_cholera
##  Length:1459                                                      
##  Class :character                                                 
##  Mode  :character                                                 
##                                                                   
##                                                                   
##                                                                   
##                                                                   
##  x13_ou_doit_on_envoyer_le_prelevement preciser_88       
##  Length:1459                           Length:1459       
##  Class :character                      Class :character  
##  Mode  :character                      Mode  :character  
##                                                          
##                                                          
##                                                          
##                                                          
##  x14_quelles_sont_les_mesures_additionnelles_a_mettre_en_place_autour_dun_cas
##  Length:1459                                                                 
##  Class :character                                                            
##  Mode  :character                                                            
##                                                                              
##                                                                              
##                                                                              
##                                                                              
##  x14_quelles_sont_les_mesures_additionnelles_a_mettre_en_place_autour_dun_cas_desinfection_des_menages
##  Min.   :0.0000                                                                                       
##  1st Qu.:1.0000                                                                                       
##  Median :1.0000                                                                                       
##  Mean   :0.9139                                                                                       
##  3rd Qu.:1.0000                                                                                       
##  Max.   :1.0000                                                                                       
##  NA's   :716                                                                                          
##  x14_quelles_sont_les_mesures_additionnelles_a_mettre_en_place_autour_dun_cas_sensibilisation_de_proximite
##  Min.   :0.0000                                                                                           
##  1st Qu.:1.0000                                                                                           
##  Median :1.0000                                                                                           
##  Mean   :0.8371                                                                                           
##  3rd Qu.:1.0000                                                                                           
##  Max.   :1.0000                                                                                           
##  NA's   :716                                                                                              
##  x14_quelles_sont_les_mesures_additionnelles_a_mettre_en_place_autour_dun_cas_chimioprophylaxie_dans_tout_le_quartier
##  Min.   :0.0000                                                                                                      
##  1st Qu.:0.0000                                                                                                      
##  Median :0.0000                                                                                                      
##  Mean   :0.4038                                                                                                      
##  3rd Qu.:1.0000                                                                                                      
##  Max.   :1.0000                                                                                                      
##  NA's   :716                                                                                                         
##  x14_quelles_sont_les_mesures_additionnelles_a_mettre_en_place_autour_dun_cas_option_4
##  Min.   :0.0000                                                                       
##  1st Qu.:0.0000                                                                       
##  Median :0.0000                                                                       
##  Mean   :0.0524                                                                       
##  3rd Qu.:0.0000                                                                       
##  Max.   :1.0000                                                                       
##  NA's   :1173                                                                         
##  x1_que_faites_vous_devant_un_cas_suspect_de_cholera
##  Length:1459                                        
##  Class :character                                   
##  Mode  :character                                   
##                                                     
##                                                     
##                                                     
##                                                     
##  x1_que_faites_vous_devant_un_cas_suspect_de_cholera_je_continue_mon_examen_sans_probleme
##  Min.   :0.0000                                                                          
##  1st Qu.:0.0000                                                                          
##  Median :0.0000                                                                          
##  Mean   :0.1208                                                                          
##  3rd Qu.:0.0000                                                                          
##  Max.   :1.0000                                                                          
##  NA's   :714                                                                             
##  x1_que_faites_vous_devant_un_cas_suspect_de_cholera_je_lui_donne_urgemment_de_la_doxycycline
##  Min.   :0.0000                                                                              
##  1st Qu.:0.0000                                                                              
##  Median :0.0000                                                                              
##  Mean   :0.2107                                                                              
##  3rd Qu.:0.0000                                                                              
##  Max.   :1.0000                                                                              
##  NA's   :714                                                                                 
##  x1_que_faites_vous_devant_un_cas_suspect_de_cholera_je_l_emmene_dans_une_salle_loin_du_reste_des_malades
##  Min.   :0.0000                                                                                          
##  1st Qu.:0.0000                                                                                          
##  Median :1.0000                                                                                          
##  Mean   :0.6819                                                                                          
##  3rd Qu.:1.0000                                                                                          
##  Max.   :1.0000                                                                                          
##  NA's   :714                                                                                             
##  x1_que_faites_vous_devant_un_cas_suspect_de_cholera_je_le_refere_dans_une_autre_fosa
##  Min.   :0.0000                                                                      
##  1st Qu.:0.0000                                                                      
##  Median :1.0000                                                                      
##  Mean   :0.6362                                                                      
##  3rd Qu.:1.0000                                                                      
##  Max.   :1.0000                                                                      
##  NA's   :714                                                                         
##  x1_que_faites_vous_devant_un_cas_suspect_de_cholera_je_ne_le_touche_pas_il_est_contagieux
##  Min.   :0.0000                                                                           
##  1st Qu.:0.0000                                                                           
##  Median :0.0000                                                                           
##  Mean   :0.0309                                                                           
##  3rd Qu.:0.0000                                                                           
##  Max.   :1.0000                                                                           
##  NA's   :714                                                                              
##  x1_que_faites_vous_devant_un_cas_suspect_de_cholera_nsp
##  Min.   :0.0000                                         
##  1st Qu.:0.0000                                         
##  Median :0.0000                                         
##  Mean   :0.0067                                         
##  3rd Qu.:0.0000                                         
##  Max.   :1.0000                                         
##  NA's   :714                                            
##  x1_que_faites_vous_devant_un_cas_suspect_de_cholera_autre preciser_102      
##  Min.   :0.0000                                            Length:1459       
##  1st Qu.:0.0000                                            Class :character  
##  Median :0.0000                                            Mode  :character  
##  Mean   :0.1248                                                              
##  3rd Qu.:0.0000                                                              
##  Max.   :1.0000                                                              
##  NA's   :714                                                                 
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera
##  Length:1459                                                    
##  Class :character                                               
##  Mode  :character                                               
##                                                                 
##                                                                 
##                                                                 
##                                                                 
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera_drsp
##  Min.   :0.0000                                                      
##  1st Qu.:0.0000                                                      
##  Median :0.0000                                                      
##  Mean   :0.0443                                                      
##  3rd Qu.:0.0000                                                      
##  Max.   :1.0000                                                      
##  NA's   :714                                                         
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera_le_chef_de_ds
##  Min.   :0.0000                                                               
##  1st Qu.:0.0000                                                               
##  Median :1.0000                                                               
##  Mean   :0.5893                                                               
##  3rd Qu.:1.0000                                                               
##  Max.   :1.0000                                                               
##  NA's   :714                                                                  
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera_le_chef_de_laire
##  Min.   :0.0000                                                                  
##  1st Qu.:0.0000                                                                  
##  Median :1.0000                                                                  
##  Mean   :0.6376                                                                  
##  3rd Qu.:1.0000                                                                  
##  Max.   :1.0000                                                                  
##  NA's   :714                                                                     
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera_01_personnel_de_la_dlmep
##  Min.   :0.0000                                                                          
##  1st Qu.:0.0000                                                                          
##  Median :0.0000                                                                          
##  Mean   :0.0268                                                                          
##  3rd Qu.:0.0000                                                                          
##  Max.   :1.0000                                                                          
##  NA's   :714                                                                             
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera_le_cpc
##  Min.   :0.0000                                                        
##  1st Qu.:0.0000                                                        
##  Median :0.0000                                                        
##  Mean   :0.0161                                                        
##  3rd Qu.:0.0000                                                        
##  Max.   :1.0000                                                        
##  NA's   :714                                                           
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera_personne_je_soigne_le_malade
##  Min.   :0.0000                                                                              
##  1st Qu.:0.0000                                                                              
##  Median :0.0000                                                                              
##  Mean   :0.0134                                                                              
##  3rd Qu.:0.0000                                                                              
##  Max.   :1.0000                                                                              
##  NA's   :714                                                                                 
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera_tous
##  Min.   :0.0000                                                      
##  1st Qu.:0.0000                                                      
##  Median :0.0000                                                      
##  Mean   :0.0148                                                      
##  3rd Qu.:0.0000                                                      
##  Max.   :1.0000                                                      
##  NA's   :714                                                         
##  x2_qui_informez_vous_de_la_presence_d_un_cas_suspect_de_cholera_nsp
##  Min.   :0.0000                                                     
##  1st Qu.:0.0000                                                     
##  Median :0.0000                                                     
##  Mean   :0.0268                                                     
##  3rd Qu.:0.0000                                                     
##  Max.   :1.0000                                                     
##  NA's   :714                                                        
##  x3_devant_un_cas_suspect_de_cholera_je_dois
##  Length:1459                                
##  Class :character                           
##  Mode  :character                           
##                                             
##                                             
##                                             
##                                             
##  x4_devant_un_cas_de_cholera_vous_devez_vous_assurer_que_les_mesures_ci_apres_soient_prises_autour_du_cas
##  Length:1459                                                                                             
##  Class :character                                                                                        
##  Mode  :character                                                                                        
##                                                                                                          
##                                                                                                          
##                                                                                                          
##                                                                                                          
##  x4_devant_un_cas_de_cholera_vous_devez_vous_assurer_que_les_mesures_ci_apres_soient_prises_autour_du_cas_donner_la_doxycycline_a_tout_le_quartier_village
##  Min.   :0.0000                                                                                                                                           
##  1st Qu.:0.0000                                                                                                                                           
##  Median :0.0000                                                                                                                                           
##  Mean   :0.2905                                                                                                                                           
##  3rd Qu.:1.0000                                                                                                                                           
##  Max.   :1.0000                                                                                                                                           
##  NA's   :712                                                                                                                                              
##  x4_devant_un_cas_de_cholera_vous_devez_vous_assurer_que_les_mesures_ci_apres_soient_prises_autour_du_cas_desinfecter_le_menage
##  Min.   :0.0000                                                                                                                
##  1st Qu.:1.0000                                                                                                                
##  Median :1.0000                                                                                                                
##  Mean   :0.9063                                                                                                                
##  3rd Qu.:1.0000                                                                                                                
##  Max.   :1.0000                                                                                                                
##  NA's   :712                                                                                                                   
##  x4_devant_un_cas_de_cholera_vous_devez_vous_assurer_que_les_mesures_ci_apres_soient_prises_autour_du_cas_chercher_la_source
##  Min.   :0.000                                                                                                              
##  1st Qu.:0.000                                                                                                              
##  Median :1.000                                                                                                              
##  Mean   :0.593                                                                                                              
##  3rd Qu.:1.000                                                                                                              
##  Max.   :1.000                                                                                                              
##  NA's   :712                                                                                                                
##  x4_devant_un_cas_de_cholera_vous_devez_vous_assurer_que_les_mesures_ci_apres_soient_prises_autour_du_cas_chercher_les_cas_additionnels
##  Min.   :0.0000                                                                                                                        
##  1st Qu.:0.0000                                                                                                                        
##  Median :1.0000                                                                                                                        
##  Mean   :0.5141                                                                                                                        
##  3rd Qu.:1.0000                                                                                                                        
##  Max.   :1.0000                                                                                                                        
##  NA's   :712                                                                                                                           
##  x4_devant_un_cas_de_cholera_vous_devez_vous_assurer_que_les_mesures_ci_apres_soient_prises_autour_du_cas_autre
##  Min.   :0.0000                                                                                                
##  1st Qu.:0.0000                                                                                                
##  Median :0.0000                                                                                                
##  Mean   :0.1071                                                                                                
##  3rd Qu.:0.0000                                                                                                
##  Max.   :1.0000                                                                                                
##  NA's   :712                                                                                                   
##  preciser_119      
##  Length:1459       
##  Class :character  
##  Mode  :character  
##                    
##                    
##                    
##                    
##  x5_pendant_une_epidemie_de_cholera_comment_doit_on_organiser_les_services_de_l_hopital
##  Length:1459                                                                           
##  Class :character                                                                      
##  Mode  :character                                                                      
##                                                                                        
##                                                                                        
##                                                                                        
##                                                                                        
##  x5_pendant_une_epidemie_de_cholera_comment_doit_on_organiser_les_services_de_l_hopital_tous_les_malades_venus_en_consultation_doivent_etre_examines_rapidement
##  Min.   :0.000                                                                                                                                                 
##  1st Qu.:0.000                                                                                                                                                 
##  Median :0.000                                                                                                                                                 
##  Mean   :0.224                                                                                                                                                 
##  3rd Qu.:0.000                                                                                                                                                 
##  Max.   :1.000                                                                                                                                                 
##  NA's   :718                                                                                                                                                   
##  x5_pendant_une_epidemie_de_cholera_comment_doit_on_organiser_les_services_de_l_hopital_le_triage_doit_etre_organise_apres_la_consultation_des_malades
##  Min.   :0.0000                                                                                                                                       
##  1st Qu.:0.0000                                                                                                                                       
##  Median :0.0000                                                                                                                                       
##  Mean   :0.2213                                                                                                                                       
##  3rd Qu.:0.0000                                                                                                                                       
##  Max.   :1.0000                                                                                                                                       
##  NA's   :718                                                                                                                                          
##  x5_pendant_une_epidemie_de_cholera_comment_doit_on_organiser_les_services_de_l_hopital_le_triage_n_est_pas_necessaire
##  Min.   :0.0000                                                                                                       
##  1st Qu.:0.0000                                                                                                       
##  Median :0.0000                                                                                                       
##  Mean   :0.0243                                                                                                       
##  3rd Qu.:0.0000                                                                                                       
##  Max.   :1.0000                                                                                                       
##  NA's   :718                                                                                                          
##  x5_pendant_une_epidemie_de_cholera_comment_doit_on_organiser_les_services_de_l_hopital_le_triage_doit_etre_organise_des_l_entree
##  Min.   :0.000                                                                                                                   
##  1st Qu.:1.000                                                                                                                   
##  Median :1.000                                                                                                                   
##  Mean   :0.776                                                                                                                   
##  3rd Qu.:1.000                                                                                                                   
##  Max.   :1.000                                                                                                                   
##  NA's   :718                                                                                                                     
##  x6_lorsqu_un_cas_de_cholera_arrive_a_la_formation_sanitaire_nous_devons
##  Length:1459                                                            
##  Class :character                                                       
##  Mode  :character                                                       
##                                                                         
##                                                                         
##                                                                         
##                                                                         
##  x1_que_faites_vous_si_vous_suspectez_un_cas_de_cholera
##  Length:1459                                           
##  Class :character                                      
##  Mode  :character                                      
##                                                        
##                                                        
##                                                        
##                                                        
##  x2_utiliseriez_vous_des_antibiotiques_pour_traiter_les_cas_de_cholera
##  Length:1459                                                          
##  Class :character                                                     
##  Mode  :character                                                     
##                                                                       
##                                                                       
##                                                                       
##                                                                       
##  x3_a_quel_moment_doit_on_mettre_le_malade_de_cholera_sous_antibiotiques
##  Length:1459                                                            
##  Class :character                                                       
##  Mode  :character                                                       
##                                                                         
##                                                                         
##                                                                         
##                                                                         
##  x4_quel_est_traitement_antibiotique_qui_peut_etre_utilise_pour_traiter_les_cas_de_cholera
##  Length:1459                                                                              
##  Class :character                                                                         
##  Mode  :character                                                                         
##                                                                                           
##                                                                                           
##                                                                                           
##                                                                                           
##  x4_quel_est_traitement_antibiotique_qui_peut_etre_utilise_pour_traiter_les_cas_de_cholera_ciprofloxacine
##  Min.   :0.0000                                                                                          
##  1st Qu.:0.0000                                                                                          
##  Median :0.0000                                                                                          
##  Mean   :0.1406                                                                                          
##  3rd Qu.:0.0000                                                                                          
##  Max.   :1.0000                                                                                          
##  NA's   :755                                                                                             
##  x4_quel_est_traitement_antibiotique_qui_peut_etre_utilise_pour_traiter_les_cas_de_cholera_metronidazole
##  Min.   :0.0000                                                                                         
##  1st Qu.:0.0000                                                                                         
##  Median :0.0000                                                                                         
##  Mean   :0.1747                                                                                         
##  3rd Qu.:0.0000                                                                                         
##  Max.   :1.0000                                                                                         
##  NA's   :755                                                                                            
##  x4_quel_est_traitement_antibiotique_qui_peut_etre_utilise_pour_traiter_les_cas_de_cholera_tetracycline
##  Min.   :0.0000                                                                                        
##  1st Qu.:0.0000                                                                                        
##  Median :0.0000                                                                                        
##  Mean   :0.1534                                                                                        
##  3rd Qu.:0.0000                                                                                        
##  Max.   :1.0000                                                                                        
##  NA's   :755                                                                                           
##  x4_quel_est_traitement_antibiotique_qui_peut_etre_utilise_pour_traiter_les_cas_de_cholera_azithromycine
##  Min.   :0.0000                                                                                         
##  1st Qu.:0.0000                                                                                         
##  Median :0.0000                                                                                         
##  Mean   :0.3196                                                                                         
##  3rd Qu.:1.0000                                                                                         
##  Max.   :1.0000                                                                                         
##  NA's   :755                                                                                            
##  x4_quel_est_traitement_antibiotique_qui_peut_etre_utilise_pour_traiter_les_cas_de_cholera_doxycycline
##  Min.   :0.0000                                                                                       
##  1st Qu.:1.0000                                                                                       
##  Median :1.0000                                                                                       
##  Mean   :0.8878                                                                                       
##  3rd Qu.:1.0000                                                                                       
##  Max.   :1.0000                                                                                       
##  NA's   :755                                                                                          
##  x5_dans_une_unite_de_prise_en_charge_du_cholera_en_plus_du_traitement_des_cas_que_doit_on_faire_pour_eviter_la_propagation_de_la_maladie
##  Length:1459                                                                                                                             
##  Class :character                                                                                                                        
##  Mode  :character                                                                                                                        
##                                                                                                                                          
##                                                                                                                                          
##                                                                                                                                          
##                                                                                                                                          
##  x6_la_surveillance_des_cas_de_cholera_se_fait
##  Length:1459                                  
##  Class :character                             
##  Mode  :character                             
##                                               
##                                               
##                                               
##                                               
##  x6_la_surveillance_des_cas_de_cholera_se_fait_toutes_les_30_min
##  Min.   :0.0000                                                 
##  1st Qu.:1.0000                                                 
##  Median :1.0000                                                 
##  Mean   :0.7972                                                 
##  3rd Qu.:1.0000                                                 
##  Max.   :1.0000                                                 
##  NA's   :744                                                    
##  x6_la_surveillance_des_cas_de_cholera_se_fait_toutes_les_heures
##  Min.   :0.000                                                  
##  1st Qu.:0.000                                                  
##  Median :0.000                                                  
##  Mean   :0.235                                                  
##  3rd Qu.:0.000                                                  
##  Max.   :1.000                                                  
##  NA's   :744                                                    
##  x6_la_surveillance_des_cas_de_cholera_se_fait_toutes_les_3h
##  Min.   :0.0000                                             
##  1st Qu.:0.0000                                             
##  Median :0.0000                                             
##  Mean   :0.0811                                             
##  3rd Qu.:0.0000                                             
##  Max.   :1.0000                                             
##  NA's   :744                                                
##  x6_la_surveillance_des_cas_de_cholera_se_fait_toutes_les_6h
##  Min.   :0.000                                              
##  1st Qu.:0.000                                              
##  Median :0.000                                              
##  Mean   :0.042                                              
##  3rd Qu.:0.000                                              
##  Max.   :1.000                                              
##  NA's   :744                                                
##  x5_aire_de_sante_141 x5_aire_de_sante_142 x1_2_par_quel_canal_143
##  Length:1459          Length:1459          Length:1459            
##  Class :character     Class :character     Class :character       
##  Mode  :character     Mode  :character     Mode  :character       
##                                                                   
##                                                                   
##                                                                   
##                                                                   
##      id_144            uuid_145         submission_time_146             
##  Min.   :253956139   Length:1459        Min.   :2023-07-19 08:44:42.00  
##  1st Qu.:254273830   Class :character   1st Qu.:2023-07-20 10:22:47.25  
##  Median :254542108   Mode  :character   Median :2023-07-21 09:42:02.50  
##  Mean   :254473106                      Mean   :2023-07-21 04:01:02.92  
##  3rd Qu.:254643004                      3rd Qu.:2023-07-21 15:38:21.25  
##  Max.   :255247114                      Max.   :2023-07-24 15:08:52.00  
##  NA's   :669                            NA's   :669                     
##  validation_status_147 notes_148       status_149        submitted_by_150
##  Mode:logical          Mode:logical   Length:1459        Mode:logical    
##  NA's:1459             NA's:1459      Class :character   NA's:1459       
##                                       Mode  :character                   
##                                                                          
##                                                                          
##                                                                          
##                                                                          
##  version_151        tags_152         index_153     record_your_current_location
##  Length:1459        Mode:logical   Min.   :  1.0   Length:1459                 
##  Class :character   NA's:1459      1st Qu.:198.2   Class :character            
##  Mode  :character                  Median :395.5   Mode  :character            
##                                    Mean   :395.5                               
##                                    3rd Qu.:592.8                               
##                                    Max.   :790.0                               
##                                    NA's   :669                                 
##  record_your_current_location_latitude record_your_current_location_longitude
##  Min.   :3.815                         Min.   : 9.630                        
##  1st Qu.:3.890                         1st Qu.: 9.726                        
##  Median :4.026                         Median : 9.753                        
##  Mean   :3.989                         Mean   :10.434                        
##  3rd Qu.:4.051                         3rd Qu.:11.512                        
##  Max.   :4.172                         Max.   :11.567                        
##  NA's   :37                            NA's   :37                            
##  record_your_current_location_altitude record_your_current_location_precision
##  Min.   : -67.83                       Min.   :   0.757                      
##  1st Qu.:  19.60                       1st Qu.:   4.266                      
##  Median :  36.65                       Median :   4.905                      
##  Mean   : 273.31                       Mean   : 185.652                      
##  3rd Qu.: 730.81                       3rd Qu.:  12.779                      
##  Max.   :1069.81                       Max.   :8993.296                      
##  NA's   :37                            NA's   :37                            
##  situation_sociogeographique_du_menage
##  Length:1459                          
##  Class :character                     
##  Mode  :character                     
##                                       
##                                       
##                                       
##                                       
##  situation_sociogeographique_du_menage_marecage
##  Min.   :0.000                                 
##  1st Qu.:0.000                                 
##  Median :0.000                                 
##  Mean   :0.285                                 
##  3rd Qu.:1.000                                 
##  Max.   :1.000                                 
##  NA's   :10                                    
##  situation_sociogeographique_du_menage_colline
##  Min.   :0.0000                               
##  1st Qu.:0.0000                               
##  Median :0.0000                               
##  Mean   :0.1567                               
##  3rd Qu.:0.0000                               
##  Max.   :1.0000                               
##  NA's   :10                                   
##  situation_sociogeographique_du_menage_quartier_precaire
##  Min.   :0.0000                                         
##  1st Qu.:0.0000                                         
##  Median :0.0000                                         
##  Mean   :0.4734                                         
##  3rd Qu.:1.0000                                         
##  Max.   :1.0000                                         
##  NA's   :10                                             
##  situation_sociogeographique_du_menage_logement_collectif_sic
##  Min.   :0.0000                                              
##  1st Qu.:0.0000                                              
##  Median :0.0000                                              
##  Mean   :0.1429                                              
##  3rd Qu.:0.0000                                              
##  Max.   :1.0000                                              
##  NA's   :10                                                  
##  situation_sociogeographique_du_menage_logement_individuel
##  Min.   :0.000                                            
##  1st Qu.:0.000                                            
##  Median :0.000                                            
##  Mean   :0.332                                            
##  3rd Qu.:1.000                                            
##  Max.   :1.000                                            
##  NA's   :10                                               
##  situation_sociogeographique_du_menage_cour_commune environnement_du_menage
##  Min.   :0.0000                                     Length:1459            
##  1st Qu.:0.0000                                     Class :character       
##  Median :0.0000                                     Mode  :character       
##  Mean   :0.2443                                                            
##  3rd Qu.:0.0000                                                            
##  Max.   :1.0000                                                            
##  NA's   :10                                                                
##  environnement_du_menage_presence_de_rigoles
##  Min.   :0.0000                             
##  1st Qu.:0.0000                             
##  Median :1.0000                             
##  Mean   :0.6355                             
##  3rd Qu.:1.0000                             
##  Max.   :1.0000                             
##  NA's   :46                                 
##  environnement_du_menage_presence_d_eaux_usees_168
##  Min.   :0.0000                                   
##  1st Qu.:0.0000                                   
##  Median :1.0000                                   
##  Mean   :0.5265                                   
##  3rd Qu.:1.0000                                   
##  Max.   :1.0000                                   
##  NA's   :46                                       
##  environnement_du_menage_presence_d_eaux_usees_169
##  Min.   :0.0000                                   
##  1st Qu.:0.0000                                   
##  Median :0.0000                                   
##  Mean   :0.3227                                   
##  3rd Qu.:1.0000                                   
##  Max.   :1.0000                                   
##  NA's   :46                                       
##  environnement_du_menage_presence_de_dechets_menagers
##  Min.   :0.0000                                      
##  1st Qu.:0.0000                                      
##  Median :0.0000                                      
##  Mean   :0.4636                                      
##  3rd Qu.:1.0000                                      
##  Max.   :1.0000                                      
##  NA's   :46                                          
##  environnement_du_menage_promiscuite localisation_du_menage
##  Min.   :0.0000                      Length:1459           
##  1st Qu.:0.0000                      Class :character      
##  Median :0.0000                      Mode  :character      
##  Mean   :0.2633                                            
##  3rd Qu.:1.0000                                            
##  Max.   :1.0000                                            
##  NA's   :46                                                
##  localisation_du_menage_pres_d_un_marche localisation_du_menage_lieu_spontane
##  Min.   :0.0000                          Min.   :0.0000                      
##  1st Qu.:0.0000                          1st Qu.:0.0000                      
##  Median :0.0000                          Median :1.0000                      
##  Mean   :0.1392                          Mean   :0.5706                      
##  3rd Qu.:0.0000                          3rd Qu.:1.0000                      
##  Max.   :1.0000                          Max.   :1.0000                      
##  NA's   :29                              NA's   :29                          
##  localisation_du_menage_grand_carrefour
##  Min.   :0.0000                        
##  1st Qu.:0.0000                        
##  Median :0.0000                        
##  Mean   :0.2021                        
##  3rd Qu.:0.0000                        
##  Max.   :1.0000                        
##  NA's   :29                            
##  localisation_du_menage_pres_d_un_espace_de_depot_hysacam
##  Min.   :0.00000                                         
##  1st Qu.:0.00000                                         
##  Median :0.00000                                         
##  Mean   :0.06643                                         
##  3rd Qu.:0.00000                                         
##  Max.   :1.00000                                         
##  NA's   :29                                              
##  localisation_du_menage_autre localisation_du_menage_option_6
##  Min.   :0.0000               Min.   :0.00000                
##  1st Qu.:0.0000               1st Qu.:0.00000                
##  Median :0.0000               Median :0.00000                
##  Mean   :0.1441               Mean   :0.03217                
##  3rd Qu.:0.0000               3rd Qu.:0.00000                
##  Max.   :1.0000               Max.   :1.00000                
##  NA's   :29                   NA's   :29                     
##  preciser_179       etat_de_la_poubelle_au_moment_de_l_enquete
##  Length:1459        Length:1459                               
##  Class :character   Class :character                          
##  Mode  :character   Mode  :character                          
##                                                               
##                                                               
##                                                               
##                                                               
##  espace_autour_de_la_poubelle types_de_dechets_deverses
##  Length:1459                  Length:1459              
##  Class :character             Class :character         
##  Mode  :character             Mode  :character         
##                                                        
##                                                        
##                                                        
##                                                        
##  types_de_dechets_deverses_restes_de_nourriture
##  Min.   :0.0000                                
##  1st Qu.:1.0000                                
##  Median :1.0000                                
##  Mean   :0.8298                                
##  3rd Qu.:1.0000                                
##  Max.   :1.0000                                
##  NA's   :72                                    
##  types_de_dechets_deverses_appareils_et_fournitures_diverses
##  Min.   :0.0000                                             
##  1st Qu.:0.0000                                             
##  Median :0.0000                                             
##  Mean   :0.3973                                             
##  3rd Qu.:1.0000                                             
##  Max.   :1.0000                                             
##  NA's   :72                                                 
##  types_de_dechets_deverses_vetements_et_assimiles
##  Min.   :0.000                                   
##  1st Qu.:0.000                                   
##  Median :0.000                                   
##  Mean   :0.434                                   
##  3rd Qu.:1.000                                   
##  Max.   :1.000                                   
##  NA's   :72                                      
##  types_de_dechets_deverses_couches_et_autres_dechets_assimiles
##  Min.   :0.0000                                               
##  1st Qu.:0.0000                                               
##  Median :1.0000                                               
##  Mean   :0.5688                                               
##  3rd Qu.:1.0000                                               
##  Max.   :1.0000                                               
##  NA's   :72                                                   
##  types_de_dechets_deverses_autre preciser_188      
##  Min.   :0.00000                 Length:1459       
##  1st Qu.:0.00000                 Class :character  
##  Median :0.00000                 Mode  :character  
##  Mean   :0.09229                                   
##  3rd Qu.:0.00000                                   
##  Max.   :1.00000                                   
##  NA's   :72                                        
##  existe_t_il_un_point_d_eau_dans_le_menage preciser_190      
##  Length:1459                               Length:1459       
##  Class :character                          Class :character  
##  Mode  :character                          Mode  :character  
##                                                              
##                                                              
##                                                              
##                                                              
##  existe_t_il_des_toilettes_dans_le_menage preciser_192       preciser_latrine
##  Length:1459                              Length:1459        Min.   :0.0000  
##  Class :character                         Class :character   1st Qu.:0.0000  
##  Mode  :character                         Mode  :character   Median :1.0000  
##                                                              Mean   :0.5372  
##                                                              3rd Qu.:1.0000  
##                                                              Max.   :1.0000  
##                                                              NA's   :20      
##  preciser_toilette_a_fosse_septique position_des_toilettes
##  Min.   :0.0000                     Length:1459           
##  1st Qu.:0.0000                     Class :character      
##  Median :1.0000                     Mode  :character      
##  Mean   :0.5177                                           
##  3rd Qu.:1.0000                                           
##  Max.   :1.0000                                           
##  NA's   :20                                               
##  distance_estimee_entre_le_puits_forage_et_les_toilettes     id_197         
##  Min.   :   0.00                                         Min.   :253044658  
##  1st Qu.:   5.00                                         1st Qu.:253266793  
##  Median :  10.00                                         Median :253553927  
##  Mean   :  69.69                                         Mean   :253698066  
##  3rd Qu.:  30.00                                         3rd Qu.:253999802  
##  Max.   :3000.00                                         Max.   :255236846  
##  NA's   :192                                                                
##    uuid_198         submission_time_199              validation_status_200
##  Length:1459        Min.   :2023-07-15 12:11:03.00   Mode:logical         
##  Class :character   1st Qu.:2023-07-16 16:32:06.50   NA's:1459            
##  Mode  :character   Median :2023-07-17 19:09:56.00                        
##                     Mean   :2023-07-18 06:46:26.22                        
##                     3rd Qu.:2023-07-19 11:22:23.50                        
##                     Max.   :2023-07-24 14:33:59.00                        
##                                                                           
##  notes_201       status_202        submitted_by_203   version_204       
##  Mode:logical   Length:1459        Length:1459        Length:1459       
##  NA's:1459      Class :character   Class :character   Class :character  
##                 Mode  :character   Mode  :character   Mode  :character  
##                                                                         
##                                                                         
##                                                                         
##                                                                         
##  tags_205         index_206     
##  Mode:logical   Min.   :   1.0  
##  NA's:1459      1st Qu.: 365.5  
##                 Median : 730.0  
##                 Mean   : 730.0  
##                 3rd Qu.:1094.5  
##                 Max.   :1459.0  
## 
unique(ebasecholera$x2_connaissez_vous_la_definition_des_cas_du_cholera)
## [1] "Non" "Oui" NA

Remplacer les valeurs manquantes de la colonne “x2_connaissez_vous_la_definition_des_cas_du_cholera” par 0

ebasecholera$x2_connaissez_vous_la_definition_des_cas_du_cholera[is.na(ebasecholera$x2_connaissez_vous_la_definition_des_cas_du_cholera)] <- 0

Puis remplacer 0 par non

ebasecholera <- ebasecholera %>% 
  mutate( x2_connaissez_vous_la_definition_des_cas_du_cholera = ifelse(
    x2_connaissez_vous_la_definition_des_cas_du_cholera == "non", "Non", x2_connaissez_vous_la_definition_des_cas_du_cholera))

verifier les valeurs

unique(ebasecholera$x3_region)
## [1] "Centre" NA

au vu du fait que dans les regions, NA(Valeur manquante) = Littoral, remplacer NA paer 0 puis o par Littoral

ebasecholera$x3_region[is.na(ebasecholera$x3_region)] <- 0
ebasecholera <- ebasecholera %>% 
  mutate( x3_region = ifelse(
    x3_region == "0", "Littoral", x3_region))

1. Verification si definition des cas correcte ou pas, mais avant, remplacer les valeurs manquantes par 0, puis 0 par Non, pusi faire le graphe

ebasecholera$definition_des_cas_corrects_ou_pas[is.na(ebasecholera$definition_des_cas_corrects_ou_pas)] <- 0
ebasecholera <- ebasecholera %>% 
  mutate( definition_des_cas_corrects_ou_pas = ifelse(definition_des_cas_corrects_ou_pas == "0", "Non", definition_des_cas_corrects_ou_pas))
ebasecholera %>%
 filter(is.na(submitted_by_203)) %>%
 ggplot() +
  aes(
    x = definition_des_cas_corrects_ou_pas,
    fill = x3_region
  ) +
  labs( x = "Reponce pour la connaissance",
        y = "niveau",
        fill = "Régions",
        title = "Verification de la definition des cas")+
  geom_bar() +
  scale_fill_hue(direction = 1) +
  theme_minimal()

summary(llcholera110124)
##     n_id_1          epiweek_date_notification_2 epiweek_date_symptoms_3
##  Length:21304       Length:21304                Length:21304           
##  Class :character   Class :character            Class :character       
##  Mode  :character   Mode  :character            Mode  :character       
##                                                                        
##                                                                        
##                                                                        
##                                                                        
##  names_and_surnames phone_number         age_year_6        sex_7          
##  Length:21304       Length:21304       Min.   :  0.00   Length:21304      
##  Class :character   Class :character   1st Qu.: 18.00   Class :character  
##  Mode  :character   Mode  :character   Median : 28.00   Mode  :character  
##                                        Mean   : 29.85                     
##                                        3rd Qu.: 40.00                     
##                                        Max.   :103.00                     
##                                        NA's   :226                        
##   profession        village_quarter    health_area_of_origin
##  Length:21304       Length:21304       Length:21304         
##  Class :character   Class :character   Class :character     
##  Mode  :character   Mode  :character   Mode  :character     
##                                                             
##                                                             
##                                                             
##                                                             
##  health_district_of_origin health_area_notifying health_district_notifying_13
##  Length:21304              Length:21304          Length:21304                
##  Class :character          Class :character      Class :character            
##  Mode  :character          Mode  :character      Mode  :character            
##                                                                              
##                                                                              
##                                                                              
##                                                                              
##  diarrhoea_oui_non_14 vomitting_oui_non_15
##  Length:21304         Length:21304        
##  Class :character     Class :character    
##  Mode  :character     Mode  :character    
##                                           
##                                           
##                                           
##                                           
##  state_of_dehydratation_1_mild_2_moderate_3_severe_16
##  Min.   :1.000                                       
##  1st Qu.:2.000                                       
##  Median :2.000                                       
##  Mean   :2.062                                       
##  3rd Qu.:3.000                                       
##  Max.   :4.000                                       
##  NA's   :1000                                        
##  date_of_onset_of_symptoms_17     date_of_consultation_18         
##  Min.   :2021-10-15 00:00:00.00   Min.   :2021-10-16 00:00:00.00  
##  1st Qu.:2022-04-04 00:00:00.00   1st Qu.:2022-04-05 00:00:00.00  
##  Median :2022-07-19 00:00:00.00   Median :2022-07-21 00:00:00.00  
##  Mean   :2022-10-22 08:19:10.43   Mean   :2022-09-18 22:35:58.68  
##  3rd Qu.:2023-04-29 00:00:00.00   3rd Qu.:2023-05-01 00:00:00.00  
##  Max.   :3034-12-03 00:00:00.00   Max.   :2024-01-09 00:00:00.00  
##                                   NA's   :1                       
##  date_of_notification_19          hospitalisation_oui_non
##  Min.   :2021-01-03 00:00:00.00   Length:21304           
##  1st Qu.:2022-04-05 00:00:00.00   Class :character       
##  Median :2022-07-22 00:00:00.00   Mode  :character       
##  Mean   :2022-09-19 05:30:27.71                          
##  3rd Qu.:2023-05-01 00:00:00.00                          
##  Max.   :2024-01-09 00:00:00.00                          
##                                                          
##  date_of_hospitalisation site_of_case_management treatment_ors_oui_no
##  Length:21304            Length:21304            Length:21304        
##  Class :character        Class :character        Class :character    
##  Mode  :character        Mode  :character        Mode  :character    
##                                                                      
##                                                                      
##                                                                      
##                                                                      
##  treatment_antibiotic_oui_no treatment_iv_liquid_oui_no treatment_zinc_oui_no
##  Length:21304                Length:21304               Length:21304         
##  Class :character            Class :character           Class :character     
##  Mode  :character            Mode  :character           Mode  :character     
##                                                                              
##                                                                              
##                                                                              
##                                                                              
##  date_of_sample_collection result_of_rdt      culture_oui_no    
##  Length:21304              Length:21304       Length:21304      
##  Class :character          Class :character   Class :character  
##  Mode  :character          Mode  :character   Mode  :character  
##                                                                 
##                                                                 
##                                                                 
##                                                                 
##  result_of_culture  date_of_discharge  outcome_2_healed_3_dead_32
##  Length:21304       Length:21304       Length:21304              
##  Class :character   Class :character   Class :character          
##  Mode  :character   Mode  :character   Mode  :character          
##                                                                  
##                                                                  
##                                                                  
##                                                                  
##  observations_facteur_de_risque_1_eau_2_assainissement_3_hygiene_4_autres_saison_surpeuplement_deplacement
##  Length:21304                                                                                             
##  Class :character                                                                                         
##  Mode  :character                                                                                         
##                                                                                                           
##                                                                                                           
##                                                                                                           
##                                                                                                           
##   region_34         commentaires_35    commentaires_36 statut_vaccinal   
##  Length:21304       Length:21304       Mode:logical    Length:21304      
##  Class :character   Class :character   NA's:21304      Class :character  
##  Mode  :character   Mode  :character                   Mode  :character  
##                                                                          
##                                                                          
##                                                                          
##                                                                          
##    x38            x39          facteurs_risque_eau_1
##  Mode:logical   Mode:logical   Mode:logical         
##  NA's:21304     NA's:21304     NA's:21304           
##                                                     
##                                                     
##                                                     
##                                                     
##                                                     
##  facteurs_risque_assainissements_2 facteurs_risque_hygiene_3
##  Mode:logical                      Mode:logical             
##  NA's:21304                        NA's:21304               
##                                                             
##                                                             
##                                                             
##                                                             
##                                                             
##  facteurs_risque_autre_4 ds_origine_44      as_origine_45        x46         
##  Mode:logical            Length:21304       Length:21304       Mode:logical  
##  NA's:21304              Class :character   Class :character   NA's:21304    
##                          Mode  :character   Mode  :character                 
##                                                                              
##                                                                              
##                                                                              
##                                                                              
##    x47          n_id_48        epiweek_date_notification_49
##  Mode:logical   Mode:logical   Mode:logical                
##  NA's:21304     NA's:21304     NA's:21304                  
##                                                            
##                                                            
##                                                            
##                                                            
##                                                            
##  epiweek_date_symptoms_50 age_year_51     sex_52        as_origine_53 
##  Mode:logical             Mode:logical   Mode:logical   Mode:logical  
##  NA's:21304               NA's:21304     NA's:21304     NA's:21304    
##                                                                       
##                                                                       
##                                                                       
##                                                                       
##                                                                       
##  ds_origine_54  health_district_notifying_55 diarrhoea_oui_non_56
##  Mode:logical   Mode:logical                 Mode:logical        
##  NA's:21304     NA's:21304                   NA's:21304          
##                                                                  
##                                                                  
##                                                                  
##                                                                  
##                                                                  
##  vomitting_oui_non_57 state_of_dehydratation_1_mild_2_moderate_3_severe_58
##  Mode:logical         Mode:logical                                        
##  NA's:21304           NA's:21304                                          
##                                                                           
##                                                                           
##                                                                           
##                                                                           
##                                                                           
##  date_of_onset_of_symptoms_59 date_of_consultation_60 date_of_notification_61
##  Mode:logical                 Mode:logical            Mode:logical           
##  NA's:21304                   NA's:21304              NA's:21304             
##                                                                              
##                                                                              
##                                                                              
##                                                                              
##                                                                              
##  outcome_2_healed_3_dead_62 region_63     
##  Mode:logical               Mode:logical  
##  NA's:21304                 NA's:21304    
##                                           
##                                           
##                                           
##                                           
## 

faire le tableau de synthèse (avec region, district le nombre de fois qu’un district a notifié en fonction de la sémaine epi, ainsi que le nombre de cas rapporté pendant la semaine) pour l’année 2023(llcholeraclean) avec nom lltableau23 et 2021, 2022 (llcholera1104244) avec nom ll tableau 2122

library(dplyr)
lltableau23 <- llcholeraclean %>%
  clean_names() %>% 
  group_by(region_34, health_district_notifying_13, epiweek_date_notification_2) %>%
  summarize(
    nombre_semaines_notifiées = n_distinct(epiweek_date_notification_2),
    nombre_de_cas = n()
  ) %>%
  arrange(region_34, health_district_notifying_13, epiweek_date_notification_2)
## `summarise()` has grouped output by 'region_34',
## 'health_district_notifying_13'. You can override using the `.groups` argument.
lltableau21_22 <- llcholera110124 %>%
  clean_names() %>% 
  group_by(region_34, date_of_notification_19, health_district_notifying_13, epiweek_date_notification_2) %>%
  summarize(
    nombre_semaines_notifiées = n_distinct(epiweek_date_notification_2),
    nombre_de_cas = n()
  ) %>%
  arrange(region_34, health_district_notifying_13, epiweek_date_notification_2)
## `summarise()` has grouped output by 'region_34', 'date_of_notification_19',
## 'health_district_notifying_13'. You can override using the `.groups` argument.

Exportation

library(openxlsx)
write.xlsx(lltableau21_22, "synthese_totale.xlsx", rowNames = FALSE)

importer les données de population et taux d’attaque

tableurtaux <- import(here("tableurtaux.xlsx")) %>% 
clean_names()
summary(tableurtaux)
##     region          date_de_notification             district_de_notification
##  Length:4473        Min.   :2021-01-03 00:00:00.00   Length:4473             
##  Class :character   1st Qu.:2022-04-24 00:00:00.00   Class :character        
##  Mode  :character   Median :2022-08-23 00:00:00.00   Mode  :character        
##                     Mean   :2022-10-21 08:21:53.48                           
##                     3rd Qu.:2023-05-14 00:00:00.00                           
##                     Max.   :2024-01-09 00:00:00.00                           
##                                                                              
##  semaine_epi        nombrede_semaines_notifiees nombre_de_cas    
##  Length:4473        Min.   :1                   Min.   :  1.000  
##  Class :character   1st Qu.:1                   1st Qu.:  1.000  
##  Mode  :character   Median :1                   Median :  2.000  
##                     Mean   :1                   Mean   :  4.516  
##                     3rd Qu.:1                   3rd Qu.:  5.000  
##                     Max.   :1                   Max.   :225.000  
##                                                                  
##  populations_ds   populations_re_g  taux_dattaque_ds    taux_dattaque_re_g 
##  Min.   : 17901   Min.   :1990710   Min.   :0.0001219   Min.   :1.899e-05  
##  1st Qu.:188293   1st Qu.:4476094   1st Qu.:0.0003122   1st Qu.:1.564e-04  
##  Median :395315   Median :4476094   Median :0.0007038   Median :5.347e-04  
##  Mean   :386481   Mean   :4247391   Mean   :0.0020607   Mean   :1.674e-03  
##  3rd Qu.:575410   3rd Qu.:5266094   3rd Qu.:0.0018261   3rd Qu.:1.405e-03  
##  Max.   :820017   Max.   :5266094   Max.   :0.1044519   Max.   :1.045e-01  
##  NA's   :1                          NA's   :1

Calculer la mediane et la representer

mediane <- tapply(tableurtaux$taux_dattaque_ds, tableurtaux$district_de_notification, median)

representation de la médiane

barplot(mediane, names.arg = names(mediane), xlab = "Districts", ylab = "Médiane du taux d'attaque")

Calculons la médiane des populations

medianepop <- tapply(tableurtaux$populations_ds, tableurtaux$district_de_notification, median)

Representation de la médiane taux d’attaque et populations en focnction des districts

medianetauxpop <- aggregate(cbind(taux_dattaque_ds, populations_ds) ~ district_de_notification, tableurtaux, median)
print(medianetauxpop)
##    district_de_notification taux_dattaque_ds populations_ds
## 1                       ABO     0.0032494487       30774.45
## 2                      awae     0.0067041654       29832.20
## 3                     BAFIA     0.0014050458      177930.14
## 4                   Bakassi     0.0080235401       37389.98
## 5                    BANGUE     0.0005059251      395315.42
## 6                BIYEM ASSI     0.0005298527      377463.39
## 7                BIYEM-ASSI     0.0002649264      377463.39
## 8                      BOKO     0.0002673915      373983.44
## 9                 BONASSAMA     0.0005278258      568369.33
## 10                     Buea     0.0007966302      188293.13
## 11                     BUEA     0.0026554341      188293.13
## 12               CITE VERTE     0.0002438974      820016.81
## 13        CITE_DES_PALMIERS     0.0002438974      820016.81
## 14                    DEIDO     0.0004683052      640607.91
## 15                DIBOMBARI     0.0022863432       43737.97
## 16                DJOUNGOLO     0.0005213677      575409.60
## 17                   Ebebda     0.0127103748       23602.77
## 18                     EDEA     0.0005448585      183533.90
## 19                  EFOULAN     0.0004165733      480107.53
## 20              Ekondo Titi     0.0114695661       61031.08
## 21               ELIGM FOMO     0.0055861561       17901.40
## 22                   JAPOMA     0.0005347423      187005.97
## 23              KUMBA NORTH     0.0007281580      137332.83
## 24              KUMBA SOUTH     0.0011115331      269897.49
## 25                    Limbe     0.0018569221      215410.22
## 26                    LIMBE     0.0037138442      215410.22
## 27                  LOGBABA     0.0007144824      279922.92
## 28                     LOUM     0.0013872576       72084.66
## 29                    MAMFE     0.0009256517      108032.00
## 30                   MANOKA     0.0032205727       31050.38
## 31                 MBALMAYO     0.0007548100      132483.67
## 32                   MBANGA     0.0011899026       84040.49
## 33                 MBANKOMO     0.0029315093       34112.12
## 34                   Mbonge     0.0010204146       97999.38
## 35                   MELONG     0.0008853779      112946.12
## 36                     MFOU     0.0008911837      112210.31
## 37                 Monatele     0.0018704338       53463.53
## 38                 MUNDEMBA     0.0042979620       23266.84
## 39                   MUYUKA     0.0016240483      123149.05
## 40                 MVOG ADA     0.0004854741      411968.38
## 41                 NEW_BELL     0.0006169628      324168.68
## 42             NJOMBE_PENJA     0.0067511107       59249.51
## 43               NKOLBISSON     0.0010392857      192439.87
## 44               NKOLNDONGO     0.0003334479      599793.91
## 45               NKONGSAMBA     0.0016406606      121902.12
## 46                     NTUI     0.0007071521      141412.29
## 47                    NYLON     0.0004321381      462814.97
## 48                    OBALA     0.0013554651      147550.83
## 49                     ODZA     0.0002258430      442785.52
## 50                    OKOLA     0.0016531824       60489.39
## 51                      Saa     0.0012993647       76960.69
## 52                      SOA     0.0040511362       49368.87
## 53                     Tiko     0.0024348054      164284.18
## 54                   TOMBEL     0.0011669295       85694.98

re-calculer la mediane de pop du DS

medianPop <- median(tableurtaux$populations_ds, na.rm = TRUE)
print(medianPop)
## [1] 395315.4

Representation graphique de la mediane

plot(tableurtaux$populations_ds, tableurtaux$taux_dattaque_ds, main = "Médiane en fonction des Populations", 
     xlab = "Population", ylab = "Taux d'attaque")
abline(h = medianPop, col = "red", lty = 2, new = TRUE)

llcholeraclean <- llcholeraclean %>% 
  mutate(sex_7 = ifelse(sex_7 == "H", "male", sex_7)) %>% 
   mutate(sex_7 = ifelse(sex_7 == "F", "female", sex_7))
  llcholeraclean$sex_7[is.na(llcholeraclean$sex_7)] <- 0
llcholeraclean <- llcholeraclean %>% 
  mutate(sex_7 =ifelse(sex_7 =="0", "male", sex_7))
llcholeraclean <- llcholeraclean %>% 
  mutate(state_of_dehydratation_1_mild_2_moderate_3_severe_16 = ifelse(state_of_dehydratation_1_mild_2_moderate_3_severe_16 == "4", "3", state_of_dehydratation_1_mild_2_moderate_3_severe_16))
llcholeraclean$age_year_6[is.na(llcholeraclean$age_year_6)] <- 28
# Transformer les données pour créer une pyramide des âges
llcholeraclean <- transform(llcholeraclean,
                            age_group = cut(age_year_6, breaks = seq(0, 100, by = 10), labels = seq(0, 95, by = 10)))

# Création du graphique
ggplot(data = llcholeraclean) +
  geom_bar(data = subset(llcholeraclean, sex_7 == "male"), aes(x = age_group, y = ..count.., fill = sex_7), position = "dodge") +
  geom_bar(data = subset(llcholeraclean, sex_7 == "female"), aes(x = age_group, y = -..count.., fill = sex_7), position = "dodge") +
  facet_grid(. ~ state_of_dehydratation_1_mild_2_moderate_3_severe_16) +
  labs(title = "Pyramide des âges en fonction du niveau de sévérité du choléra",
       x = "Âge",
       y = "Nombre de cas",
       fill = "Sexe") +
  scale_y_continuous(labels = abs, breaks = seq(-90, 175, by = 40)) +  
  # Pour afficher les valeurs absolues sur l'axe y
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=2))  
## Warning: The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(count)` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

# Pour faire pivoter les étiquettes d'âge

Modélisation de la persistance

Étape 1 : Préparation des données Assurez-vous que vos données sont chargées dans R et qu’elles sont prêtes pour l’analyse.

Étape 2 : Modélisation de la persistance temporelle Utilisez un modèle de régression pour examiner la relation entre le nombre de cas de choléra et le temps (en semaines épidémiologiques) pour chaque région. Vous pouvez utiliser la fonction lm() pour ajuster un modèle linéaire. #1 Centre

donnee_centre <- subset(llcholeraclean, region_34 == "Centre")
modele_centre <- lm(cas ~ epiweek_date_notification_2, data = donnee_centre)

donnee_centre$epiweek_date_notification_2 <- as.numeric(donnee_centre$epiweek_date_notification_2)
## Warning: NAs introduced by coercion
summary(modele_centre)
## 
## Call:
## lm(formula = cas ~ epiweek_date_notification_2, data = donnee_centre)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -0.9865  0.0000  0.0000  0.0000  0.5000 
## 
## Coefficients:
##                                       Estimate Std. Error t value Pr(>|t|)    
## (Intercept)                          1.000e+00  1.118e-02  89.413   <2e-16 ***
## epiweek_date_notification_2S04_2023  9.056e-13  1.370e-02   0.000    1.000    
## epiweek_date_notification_2S05_2023  9.055e-13  1.250e-02   0.000    1.000    
## epiweek_date_notification_2S06_2023  9.056e-13  1.582e-02   0.000    1.000    
## epiweek_date_notification_2S07_2023  9.055e-13  2.740e-02   0.000    1.000    
## epiweek_date_notification_2S08_2023  9.055e-13  2.740e-02   0.000    1.000    
## epiweek_date_notification_2S11_2023  9.056e-13  2.740e-02   0.000    1.000    
## epiweek_date_notification_2S12_2023  9.056e-13  2.092e-02   0.000    1.000    
## epiweek_date_notification_2S13_2023  9.056e-13  1.272e-02   0.000    1.000    
## epiweek_date_notification_2S14_2023  9.056e-13  1.161e-02   0.000    1.000    
## epiweek_date_notification_2S15_2023  9.056e-13  1.176e-02   0.000    1.000    
## epiweek_date_notification_2S16_2023  9.056e-13  1.130e-02   0.000    1.000    
## epiweek_date_notification_2S17_2023  9.056e-13  1.124e-02   0.000    1.000    
## epiweek_date_notification_2S18_2023  9.055e-13  1.126e-02   0.000    1.000    
## epiweek_date_notification_2S19_2023  9.055e-13  1.124e-02   0.000    1.000    
## epiweek_date_notification_2S20_2023  9.056e-13  1.124e-02   0.000    1.000    
## epiweek_date_notification_2S21_2023  9.056e-13  1.125e-02   0.000    1.000    
## epiweek_date_notification_2S22_2023  9.056e-13  1.124e-02   0.000    1.000    
## epiweek_date_notification_2S23_2023  9.055e-13  1.127e-02   0.000    1.000    
## epiweek_date_notification_2S24_2023  9.055e-13  1.128e-02   0.000    1.000    
## epiweek_date_notification_2S25_2023  9.057e-13  1.140e-02   0.000    1.000    
## epiweek_date_notification_2S26_2023  9.056e-13  1.149e-02   0.000    1.000    
## epiweek_date_notification_2S27_2023  9.058e-13  1.163e-02   0.000    1.000    
## epiweek_date_notification_2S28_2023  9.056e-13  1.172e-02   0.000    1.000    
## epiweek_date_notification_2S29_2023  9.058e-13  1.173e-02   0.000    1.000    
## epiweek_date_notification_2S30_2023  9.056e-13  1.169e-02   0.000    1.000    
## epiweek_date_notification_2S31_2023  9.059e-13  1.161e-02   0.000    1.000    
## epiweek_date_notification_2S32_2023  9.056e-13  1.171e-02   0.000    1.000    
## epiweek_date_notification_2S33_2023  9.057e-13  1.190e-02   0.000    1.000    
## epiweek_date_notification_2S34_2023  9.057e-13  1.211e-02   0.000    1.000    
## epiweek_date_notification_2S35_2023  9.056e-13  1.250e-02   0.000    1.000    
## epiweek_date_notification_2S36_2023  9.054e-13  1.370e-02   0.000    1.000    
## epiweek_date_notification_2S37_2023 -1.351e-02  1.156e-02  -1.169    0.242    
## epiweek_date_notification_2S38_2023  9.056e-13  1.186e-02   0.000    1.000    
## epiweek_date_notification_2S39_2023  9.055e-13  1.214e-02   0.000    1.000    
## epiweek_date_notification_2S40_2023  9.057e-13  1.244e-02   0.000    1.000    
## epiweek_date_notification_2S41_2023  9.055e-13  1.229e-02   0.000    1.000    
## epiweek_date_notification_2S42_2023  9.059e-13  1.264e-02   0.000    1.000    
## epiweek_date_notification_2S43_2023  9.057e-13  1.331e-02   0.000    1.000    
## epiweek_date_notification_2S44_2023  9.058e-13  1.303e-02   0.000    1.000    
## epiweek_date_notification_2S45_2023  9.052e-13  1.514e-02   0.000    1.000    
## epiweek_date_notification_2S46_2023  9.049e-13  1.349e-02   0.000    1.000    
## epiweek_date_notification_2S47_2023  9.053e-13  1.582e-02   0.000    1.000    
## epiweek_date_notification_2S48_2023 -2.857e-01  1.464e-02 -19.512   <2e-16 ***
## epiweek_date_notification_2S49_2023 -5.000e-01  2.092e-02 -23.897   <2e-16 ***
## epiweek_date_notification_2S50_2023  9.050e-13  2.092e-02   0.000    1.000    
## epiweek_date_notification_2S51_2023  9.050e-13  1.678e-02   0.000    1.000    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.02501 on 4661 degrees of freedom
## Multiple R-squared:  0.2706, Adjusted R-squared:  0.2634 
## F-statistic: 37.59 on 46 and 4661 DF,  p-value: < 2.2e-16
plot(donnee_centre$epiweek_date_notification_2, donnee_centre$cas, 
     xlab = "Semaines épidémiologiques", ylab = "Nombre de cas", 
     main = "Tracé des cas de choléra par semaine (Centre)", 
     xlim = c(1, 52), ylim = range(donnee_centre$cas))

# Ajouter la ligne de régression
abline(modele_centre, col = "red")
## Warning in abline(modele_centre, col = "red"): only using the first two of 47
## regression coefficients

#2 Littoral

donnee_littoral <- subset(llcholeraclean, region_34 == "Littoral")
modele_littoral <- lm(cas ~ epiweek_date_notification_2, data = donnee_littoral)
summary(modele_littoral)
## 
## Call:
## lm(formula = cas ~ epiweek_date_notification_2, data = donnee_littoral)
## 
## Residuals:
##        Min         1Q     Median         3Q        Max 
## -5.570e-15  0.000e+00  0.000e+00  0.000e+00  3.791e-13 
## 
## Coefficients:
##                                       Estimate Std. Error   t value Pr(>|t|)
## (Intercept)                          1.000e+00  2.449e-15 4.083e+14   <2e-16
## epiweek_date_notification_2S02_2023 -4.134e-28  3.644e-15 0.000e+00   1.0000
## epiweek_date_notification_2S03_2023 -3.060e-28  3.907e-15 0.000e+00   1.0000
## epiweek_date_notification_2S04_2023 -4.029e-28  4.330e-15 0.000e+00   1.0000
## epiweek_date_notification_2S05_2023 -3.445e-28  3.517e-15 0.000e+00   1.0000
## epiweek_date_notification_2S06_2023 -5.893e-29  3.464e-15 0.000e+00   1.0000
## epiweek_date_notification_2S07_2023 -5.255e-29  3.907e-15 0.000e+00   1.0000
## epiweek_date_notification_2S08_2023 -3.507e-28  3.721e-15 0.000e+00   1.0000
## epiweek_date_notification_2S09_2023 -1.981e-28  3.371e-15 0.000e+00   1.0000
## epiweek_date_notification_2S10_2023 -1.844e-28  4.330e-15 0.000e+00   1.0000
## epiweek_date_notification_2S11_2023 -3.365e-28  4.163e-15 0.000e+00   1.0000
## epiweek_date_notification_2S12_2023 -2.994e-28  5.137e-15 0.000e+00   1.0000
## epiweek_date_notification_2S13_2023 -1.711e-28  3.807e-15 0.000e+00   1.0000
## epiweek_date_notification_2S14_2023 -3.824e-28  4.024e-15 0.000e+00   1.0000
## epiweek_date_notification_2S15_2023 -3.095e-28  3.464e-15 0.000e+00   1.0000
## epiweek_date_notification_2S16_2023 -3.076e-28  4.163e-15 0.000e+00   1.0000
## epiweek_date_notification_2S17_2023 -2.796e-28  3.415e-15 0.000e+00   1.0000
## epiweek_date_notification_2S18_2023 -2.082e-28  3.261e-15 0.000e+00   1.0000
## epiweek_date_notification_2S19_2023  1.820e-28  3.415e-15 0.000e+00   1.0000
## epiweek_date_notification_2S20_2023 -5.560e-28  3.015e-15 0.000e+00   1.0000
## epiweek_date_notification_2S21_2023 -5.081e-28  3.261e-15 0.000e+00   1.0000
## epiweek_date_notification_2S22_2023 -6.656e-28  3.517e-15 0.000e+00   1.0000
## epiweek_date_notification_2S23_2023  2.850e-29  4.330e-15 0.000e+00   1.0000
## epiweek_date_notification_2S24_2023 -1.744e-28  3.644e-15 0.000e+00   1.0000
## epiweek_date_notification_2S25_2023 -3.005e-28  4.024e-15 0.000e+00   1.0000
## epiweek_date_notification_2S26_2023 -1.741e-28  6.324e-15 0.000e+00   1.0000
## epiweek_date_notification_2S27_2023 -6.608e-28  4.535e-15 0.000e+00   1.0000
## epiweek_date_notification_2S28_2023 -2.090e-28  3.261e-15 0.000e+00   1.0000
## epiweek_date_notification_2S29_2023 -6.024e-28  4.163e-15 0.000e+00   1.0000
## epiweek_date_notification_2S30_2023  5.575e-15  2.734e-15 2.039e+00   0.0416
## epiweek_date_notification_2S31_2023 -2.596e-28  2.935e-15 0.000e+00   1.0000
## epiweek_date_notification_2S32_2023 -3.098e-28  2.835e-15 0.000e+00   1.0000
## epiweek_date_notification_2S33_2023 -1.405e-28  2.821e-15 0.000e+00   1.0000
## epiweek_date_notification_2S34_2023 -1.667e-28  2.583e-15 0.000e+00   1.0000
## epiweek_date_notification_2S35_2023 -2.308e-28  2.614e-15 0.000e+00   1.0000
## epiweek_date_notification_2S36_2023 -2.924e-28  2.657e-15 0.000e+00   1.0000
## epiweek_date_notification_2S37_2023 -2.627e-28  2.686e-15 0.000e+00   1.0000
## epiweek_date_notification_2S38_2023 -3.324e-28  2.645e-15 0.000e+00   1.0000
## epiweek_date_notification_2S39_2023 -2.543e-28  2.694e-15 0.000e+00   1.0000
## epiweek_date_notification_2S40_2023 -3.135e-28  2.858e-15 0.000e+00   1.0000
## epiweek_date_notification_2S41_2023 -2.752e-28  3.015e-15 0.000e+00   1.0000
## epiweek_date_notification_2S42_2023 -2.834e-28  3.174e-15 0.000e+00   1.0000
## epiweek_date_notification_2S43_2023 -2.944e-28  3.230e-15 0.000e+00   1.0000
## epiweek_date_notification_2S44_2023 -2.499e-28  3.371e-15 0.000e+00   1.0000
## epiweek_date_notification_2S45_2023 -3.188e-28  3.261e-15 0.000e+00   1.0000
## epiweek_date_notification_2S46_2023 -2.493e-28  5.612e-15 0.000e+00   1.0000
## epiweek_date_notification_2S47_2023 -3.196e-28  3.807e-15 0.000e+00   1.0000
## epiweek_date_notification_2S48_2023 -2.893e-28  3.464e-15 0.000e+00   1.0000
## epiweek_date_notification_2S49_2023 -2.916e-28  4.024e-15 0.000e+00   1.0000
## epiweek_date_notification_2S50_2023 -2.931e-28  4.330e-15 0.000e+00   1.0000
## epiweek_date_notification_2S51_2023 -2.911e-28  3.807e-15 0.000e+00   1.0000
## epiweek_date_notification_2S52_2023 -3.233e-28  4.795e-15 0.000e+00   1.0000
##                                        
## (Intercept)                         ***
## epiweek_date_notification_2S02_2023    
## epiweek_date_notification_2S03_2023    
## epiweek_date_notification_2S04_2023    
## epiweek_date_notification_2S05_2023    
## epiweek_date_notification_2S06_2023    
## epiweek_date_notification_2S07_2023    
## epiweek_date_notification_2S08_2023    
## epiweek_date_notification_2S09_2023    
## epiweek_date_notification_2S10_2023    
## epiweek_date_notification_2S11_2023    
## epiweek_date_notification_2S12_2023    
## epiweek_date_notification_2S13_2023    
## epiweek_date_notification_2S14_2023    
## epiweek_date_notification_2S15_2023    
## epiweek_date_notification_2S16_2023    
## epiweek_date_notification_2S17_2023    
## epiweek_date_notification_2S18_2023    
## epiweek_date_notification_2S19_2023    
## epiweek_date_notification_2S20_2023    
## epiweek_date_notification_2S21_2023    
## epiweek_date_notification_2S22_2023    
## epiweek_date_notification_2S23_2023    
## epiweek_date_notification_2S24_2023    
## epiweek_date_notification_2S25_2023    
## epiweek_date_notification_2S26_2023    
## epiweek_date_notification_2S27_2023    
## epiweek_date_notification_2S28_2023    
## epiweek_date_notification_2S29_2023    
## epiweek_date_notification_2S30_2023 *  
## epiweek_date_notification_2S31_2023    
## epiweek_date_notification_2S32_2023    
## epiweek_date_notification_2S33_2023    
## epiweek_date_notification_2S34_2023    
## epiweek_date_notification_2S35_2023    
## epiweek_date_notification_2S36_2023    
## epiweek_date_notification_2S37_2023    
## epiweek_date_notification_2S38_2023    
## epiweek_date_notification_2S39_2023    
## epiweek_date_notification_2S40_2023    
## epiweek_date_notification_2S41_2023    
## epiweek_date_notification_2S42_2023    
## epiweek_date_notification_2S43_2023    
## epiweek_date_notification_2S44_2023    
## epiweek_date_notification_2S45_2023    
## epiweek_date_notification_2S46_2023    
## epiweek_date_notification_2S47_2023    
## epiweek_date_notification_2S48_2023    
## epiweek_date_notification_2S49_2023    
## epiweek_date_notification_2S50_2023    
## epiweek_date_notification_2S51_2023    
## epiweek_date_notification_2S52_2023    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.01e-14 on 1430 degrees of freedom
## Multiple R-squared:  0.4999, Adjusted R-squared:  0.4821 
## F-statistic: 28.03 on 51 and 1430 DF,  p-value: < 2.2e-16

#3 Sud-Ouest

donnee_sud_ouest <- subset(llcholeraclean, region_34 == "Sud-Ouest")
modele_sud_ouest <- lm(cas ~ epiweek_date_notification_2, data = donnee_sud_ouest)
summary(modele_sud_ouest)
## 
## Call:
## lm(formula = cas ~ epiweek_date_notification_2, data = donnee_sud_ouest)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.95455  0.00000  0.00000  0.00000  0.04545 
## 
## Coefficients:
##                                       Estimate Std. Error t value Pr(>|t|)    
## (Intercept)                          1.000e+00  8.704e-02  11.489   <2e-16 ***
## epiweek_date_notification_2S33_2023 -4.184e-14  8.891e-02   0.000     1.00    
## epiweek_date_notification_2S34_2023 -4.187e-14  8.989e-02   0.000     1.00    
## epiweek_date_notification_2S35_2023 -4.182e-14  9.305e-02   0.000     1.00    
## epiweek_date_notification_2S36_2023 -4.186e-14  8.839e-02   0.000     1.00    
## epiweek_date_notification_2S37_2023 -4.188e-14  9.731e-02   0.000     1.00    
## epiweek_date_notification_2S38_2023 -4.185e-14  9.305e-02   0.000     1.00    
## epiweek_date_notification_2S39_2023 -4.190e-14  1.231e-01   0.000     1.00    
## epiweek_date_notification_2S40_2023 -4.189e-14  1.066e-01   0.000     1.00    
## epiweek_date_notification_2S41_2023 -4.188e-14  9.059e-02   0.000     1.00    
## epiweek_date_notification_2S42_2023 -4.545e-02  8.900e-02  -0.511     0.61    
## epiweek_date_notification_2S43_2023 -4.186e-14  9.535e-02   0.000     1.00    
## epiweek_date_notification_2S44_2023 -4.186e-14  9.401e-02   0.000     1.00    
## epiweek_date_notification_2S45_2023 -4.185e-14  1.231e-01   0.000     1.00    
## epiweek_date_notification_2S46_2023 -4.185e-14  1.005e-01   0.000     1.00    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.08704 on 126 degrees of freedom
## Multiple R-squared:  0.03864,    Adjusted R-squared:  -0.06818 
## F-statistic: 0.3617 on 14 and 126 DF,  p-value: 0.9829